10 |
11 | {{ content }}
12 |
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/_posts/2015-06-09-api.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | title: "Common URL API"
5 | order: 0
6 | ---
7 |
8 | The NCBI-BLAST Common URL API allows you to run searches remotely. It supports the same
9 | commands at the NCBI web server and at a cloud provider installation. This allows you to switch from
10 | running searches at the NCBI web server to a cloud provider (or *visa versa*) with minimal effort.
11 | Every call to the Common URL API must include the `CMD` parameter, which can take one of four different
12 | arguments. You may use `Put` for search submission, `Get` for checking the
13 | status of a submission or retrieving results, `Delete` to remove a search and
14 | its results or `DisplayRIDs` to list all RIDs in the system. Each argument to
15 | `CMD` requires or allows certain other parameters as described in the table below.
16 | The table below lists _all_ supported parameters. Other parameters are not supported and should not be
17 | relied upon by users of the URL API. An asterisk (*) in the `CMD` column indicates that the parameter is
18 | required for that command.
19 |
20 | Also, see the information at [Running Web BLAST]({{ site.baseurl }}{% post_url 2015-06-09-running-web-blast %}) and
21 | [authentication]({{ site.baseurl }}{% post_url 2015-06-09-authentication %}).
22 |
23 |
24 | |Parameter | Definition | Type | CMD | Allowed values |
25 | |-----------------------|-------------------------|------|-----|--------------------------------|
26 | |`QUERY`|Search query|String|Put *|Accession, GI, or FASTA.|
27 | |`DATABASE`|BLAST database|String|Put *|Database from appendix 2 or one uploaded to blastdb_custom (see appendix 4)|
28 | |`PROGRAM`|BLAST program|String|Put *|One of blastn, blastp, blastx, tblastn, tblastx. To enable megablast, use `PROGRAM=blastn&MEGABLAST=on`.|
29 | |`FILTER`|Low complexity filtering|String|Put |F to disable. T or L to enable. Prepend "m" for mask at lookup (e.g., mL)|
30 | |`FORMAT_TYPE`|Report type|String|Put, Get| HTML, Text, XML, XML2, JSON2, or Tabular. HTML is the default.|
31 | |`EXPECT`|Expect value|Double|Put|Number greater than zero.|
32 | |`NUCL_REWARD`|Reward for matching bases (BLASTN and megaBLAST)|Integer|Put|Integer greater than zero.|
33 | |`NUCL_PENALTY`|Cost for mismatched bases (BLASTN and megaBLAST)|Integer|Put|Integer less than zero.|
34 | |`GAPCOSTS`|Gap existence and extension costs|String|Put|Pair of positive integers separated by a space such as "11 1".|
35 | |`MATRIX`|Scoring matrix name|String|Put|One of BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, PAM250, PAM30 or PAM70. Default: BLOSUM62 for all applicable programs|
36 | |`HITLIST_SIZE`|Number of databases sequences to keep| Integer|Put,Get| Integer greater than zero.|
37 | |`DESCRIPTIONS`|Number of descriptions to print (applies to HTML and Text)| Integer|Put,Get| Integer greater than zero.|
38 | |`ALIGNMENTS`|Number of alignments to print (applies to HTML and Text)| Integer|Put,Get| Integer greater than zero.|
39 | |`NCBI_GI`|Show NCBI GIs in report|String|Put, Get|T or F|
40 | |`RID`|BLAST search request identifier|String|Get *, Delete *|The Request ID (RID) returned when the search was submitted|
41 | |`THRESHOLD`|Neighboring score for initial words|Integer | Put | Positive integer (BLASTP default is 11). Does not apply to BLASTN or MegaBLAST).|
42 | |`WORD_SIZE`|Size of word for initial matches| Integer| Put | Positive integer.|
43 | |`COMPOSITION_BASED_STATISTICS`| Composition based statistics algorithm to use| Integer | Put| One of 0, 1, 2, or 3. See `comp_based_stats` command line option in the [BLAST+ user manual](https://www.ncbi.nlm.nih.gov/books/NBK279675/) for details.|
44 | |`FORMAT_OBJECT`|Object type| String | Get | SearchInfo (status check) or Alignment (report formatting).|
45 | |`NUM_THREADS`| Number of virtual CPUs to use| Integer | Put | Integer greater than zero and less than the maximum number of cores on the instance (default is the maximum number of cores on the instance). **Supported only on the cloud** |
46 |
47 |
48 | If a parameter is not required and not provided, then the default value will be
49 | used. That default value may depend upon the BLAST search you are running.
50 |
51 |
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/_posts/2015-06-09-authentication.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Web server authentication"
5 | order: 3
6 | ---
7 |
8 | In order to access [a running instance via a web browser]({{ site.baseurl }}{% post_url 2015-06-09-running-web-blast %})
9 | or programmatically via the [NCBI-BLAST Common URL API interface]({{ site.baseurl }}{% post_url 2015-06-09-api %}), one
10 | needs to provide credentials.
11 |
12 | The user name is set to `blast` and the password is the AWS instance ID.
13 |
14 | A web browser will prompt for credentials (see screenshot below); programmatic
15 | access will require authentication to be configured. For example, assuming the instance's
16 | ID is `i-01ef8ea68031299de` and its public DNS is `ec2-54-90-191-42.compute-1.amazonaws.com`:
17 |
18 |
19 | ```
20 | $ curl http://blast:i-01ef8ea68031299de@ec2-54-90-191-42.compute-1.amazonaws.com/cgi-bin/blast.cgi
21 | ```
22 |
23 |
24 | Please consult the appropriate tool/API's documentation to properly configure programmatic access.
25 |
26 |
27 |
28 | 
29 |
30 |
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/_posts/2015-06-09-available-blastdbs-gcp.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Available BLAST databases in GCP"
5 | order: 6
6 | ---
7 |
8 | The following BLAST databases are available in Google Cloud Storage (GCS) (data as of December 6, 2018). You can obtain an updated list of BLAST databases by running `update_blastdb.pl --showall pretty --source gcp`.
9 |
10 | If working on GCP, you can get these BLASTDBs following these instructions:
11 | * if you have BLAST+ installed, see [Get NCBI BLAST databases](https://www.ncbi.nlm.nih.gov/books/NBK537770/) in the BLAST+ user manual.
12 | * Otherwise, if you have docker, follow [these instructions](https://github.com/ncbi/blast_plus_docs#show-blast-databases-available-for-download-from-the-google-cloud-bucket).
13 |
14 | |Name |Title |Size (GB)|Last updated|
15 | |--------|---------------------|---------|------------|
16 | GPIPE/10090/106/GCF_000001635.24_top_level|Mus musculus GRCm38.p4 [GCF_000001635.24] chromosomes plus unplaced and unlocalized scaffolds| 1.3150|2016-06-22
17 | GPIPE/9606/109/GCF_000001405.38_top_level|Homo sapiens GRCh38.p12 [GCF_000001405.38] chromosomes plus unplaced and unlocalized scaffolds| 1.5668|2018-03-28
18 | SMARTBLAST/landmark_v5|Landmark database for SmartBLAST| 0.3628|2018-12-03
19 | genomic/Viruses/NCBI_VIV_nucleotide_sequences_v5|NCBI VIV nucleotide sequences| 62.6420|2018-12-04
20 | genomic/Viruses/NCBI_VIV_protein_sequences_v5|NCBI VIV protein sequences| 205.8316|2018-12-04
21 | nr_v5|All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects| 205.8268|2018-12-03
22 | nt_v5|Nucleotide collection (nt)| 62.6412|2018-12-03
23 | pdb_v5|PDB protein database| 0.1357|2018-12-04
24 | rRNA_typestrains/prokaryotic_16S_ribosomal_RNA_v5|16S ribosomal RNA (Bacteria and Archaea)| 62.6413|2018-12-04
25 | ref_viroids_rep_genomes_v5|Refseq viroids representative genomes| 0.0001|2018-12-03
26 | ref_viruses_rep_genomes_v5|Refseq viruses representative genomes| 0.0698|2018-12-03
27 | refseq_protein_v5|NCBI Protein Reference Sequences| 205.8493|2018-12-04
28 | refseq_rna_v5|NCBI Transcript Reference Sequences| 62.6473|2018-12-04
29 | swissprot_v5|Non-redundant UniProtKB/SwissProt sequences| 0.3575|2018-12-04
30 | taxdb|Taxonomy BLAST databases| 0.1479|2018-12-03
31 |
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/_posts/2015-06-09-available-blastdbs.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Available BLAST databases"
5 | order: 0
6 | ---
7 |
8 | |Name |Title |Type|
9 | |--------|---------------------|----|
10 | |nt |Nucleotide collection|DNA |
11 | |nr |Non-redundant |Protein|
12 | |refseq_rna|NCBI Transcript Reference Sequences|DNA|
13 | |refseq_protein|NCBI Protein Reference Sequences|Protein|
14 | |swissprot|Non-redundant UniProtKB/SwissProt sequences|Protein|
15 | |pdbaa|PDB protein database|Protein|
16 | |pdbnt|PDB nucleotide database|DNA|
17 |
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/_posts/2015-06-09-choosing-instance.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: conf
4 | title: "How to choose an instance?"
5 | order: 0
6 | ---
7 |
8 | **NOTE**: If you intend to stop and re-start an instance, please choose an AWS
9 | instance type that has EBS as its storage. If SSDs are used, their contents (i.e.: any BLAST results and custom BLAST databases)
10 | will be lost after the instance is rebooted or restarted.
11 | If EBS storage is used, by default the BLAST AMI starts up with a 300GB EBS drive.
12 |
13 | ### BLAST performance
14 |
15 | BLAST performs best when the BLAST database's sequence data can fit into RAM (see section below), so BLAST
16 | searches will not run efficiently on smaller instances. Please see your cloud
17 | provider for a [list of suitable instances](https://aws.amazon.com/ec2/instance-types/).
18 |
19 | ### BLAST database storage
20 |
21 | The server image is designed to use a local "scratch" disk to speed up the
22 | BLAST database. For AWS, you need to ensure that your instance has 'instance
23 | storage' and that it is attached.
24 |
25 | The nucleotide `nt` database contains about 174 billion bases, but
26 | the sequence data is compressed 4-to-1. Hence, the sequences require about 42
27 | GB. The protein `nr` database contains about 54 billion residues, so
28 | the sequences require 51 GB. The *total* size of the `nt` database as of this
29 | writing (03/15/2018) is 54 GB and the size of `nr` is 154 GB.
30 | Please be sure to provision an instance with enough RAM and disk space for the BLAST
31 | database(s) you will be using.
32 |
33 | The instance downloads BLAST databases with a [FUSE client]({{ site.baseurl }}{% post_url 2015-06-09-fuse %})
34 | from the NCBI during the first search of that database. This means that the
35 | first BLAST search will be slow, but afterwards the database will be cached locally
36 | and BLAST will run faster.
37 |
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/_posts/2015-06-09-copyright.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | order: 3
5 | ---
6 | With the exception of certain third-party files summarized below, this software is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.
7 |
8 | Please cite the authors in any work or product based on this material [1, 2].
9 |
10 | 1. NCBI Resource Coordinators. Database resources of the National Center for
11 | Biotechnology Information. Nucleic Acids Res. 2013 Jan;41(Database issue):D8-D20.
12 | doi: 10.1093/nar/gks1189. Epub 2012 Nov 27. PubMed PMID: 23193264; PubMed Central PMCID: PMC3531099.
13 |
14 | 1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.
15 | BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PubMed PMID: 20003500; PubMed Central PMCID: PMC2803857.
16 |
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/_posts/2015-06-09-cost.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: intro
4 | title: "Cost"
5 | order: 3
6 | ---
7 |
8 | NCBI does not charge for the use of our software but you will be billed by the
9 | cloud provider. All costs associated with running the BLAST+ software in a
10 | cloud provider are your own responsibility. Please ensure that you delete any
11 | resources you are not using. The cloud providers all provide alerting services
12 | to avoid unexpectedly large charges, NCBI suggests that you use these services.
13 |
14 | For AWS, please see the [EC2 documentation](http://docs.amazonwebservices.com/AWSEC2/latest/GettingStartedGuide/) [at AWS](http://aws.amazon.com/getting-started/) and their [pricing information](https://aws.amazon.com/ec2/pricing/). AWS also provides a [Command Line Interface](https://aws.amazon.com/cli/).
15 |
16 |
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/_posts/2015-06-09-custom-blastdbs.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Custom BLAST databases"
5 | order: 2
6 | ---
7 |
8 | After you have [created your own BLAST
9 | databases](https://www.ncbi.nlm.nih.gov/books/NBK279688/), to make them
10 | available in the BLAST AMI, simply copy your BLAST database files onto the
11 | instance's `/blast/blastdb_custom` directory. E.g.:
12 |
13 | scp -i ubuntu@:/blast/blastdb_custom/
14 |
15 |
16 | These (and any other) BLAST databases installed in the `/blast/blastdb_custom`
17 | directory in the instance will be immediately available for searching via the
18 | URL API, web interface, and BLAST+ command line applications on that instance.
19 |
20 |
21 | **If you run into any difficulty, please feel free to email us at blast-help@ncbi.nlm.nih.gov so we can help you!**
22 |
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/_posts/2015-06-09-data-center-location.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: conf
4 | title: "How to choose a region?"
5 | order: 2
6 | ---
7 |
8 | Since the [BLAST databases]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %}) are fetched from the NCBI, downloads are faster if the
9 | instance runs in a region that is geographically close to NCBI. NCBI is located in the east coast of North America.
10 |
11 | For AWS, `us-east-1` (N. Virginia) is the closest region, so for optimal download performance, please consider
12 | starting your instance in that region. You can find a list of available AWS regions [here](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-regions-availability-zones.html).
13 |
14 | In other cases, such as `us-west-1` (N. California) and `eu-west-1` (Ireland), *downloading the BLAST databases can take a few hours*.
15 |
16 |
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/_posts/2015-06-09-disclaimer.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | order: 4
5 | ---
6 |
7 | Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, The NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.
8 |
9 | There are a number of known issues and limitations to the approach described here. They are listed below.
10 |
11 | There is no load balancing in the current AMI. A number of users running searches at the same time could overload an instance. The NCBI hopes to address this in a future version.
12 |
13 | It is possible that searches at an AWS instance could produce different results than those at the NCBI BLAST website. The different results could be caused by differences in the version of the software, BLAST database, or other issues beyond the control of the NCBI.
14 |
15 | A running instance will download BLAST databases from the NCBI. The instance will normally place minimal demands on the NCBI website since the database is cached after the first download. Use of an instance in a manner that places heavy demands on the NCBI site may result in the instance being blocked.
16 |
17 | The BLAST results and databases are kept on ephemeral storage at AWS. User error (e.g., premature stopping or termination of an instance) could result in loss of data. Problems at AWS or with NCBI software could also result in the loss of data.
18 |
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/_posts/2015-06-09-exceptions.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | order: 5
5 | ---
6 | Location: configure
7 | Authors: Free Software Foundation, Inc.
8 | License: Unrestricted; at top of file
9 |
10 | Location: config.guess, config.sub
11 | Authors: FSF
12 | License: Unrestricted when distributed with the Toolkit; standalone, GNU General Public License [`gpl.txt`]
13 |
14 | Location: `{src,include}/dbapi/driver/ftds*/freetds`
15 | Authors: See `src/dbapi/driver/ftds*/freetds/AUTHORS`
16 | License: GNU Library/Lesser General Public License [`src/dbapi/driver/ftds*/freetds/COPYING.LIB`]
17 |
18 | Location: `include/dbapi/driver/odbc/unix_odbc`
19 | Authors: Peter Harvey and Nick Gorham
20 | License: GNU LGPL
21 |
22 | Location: `{src,include}/gui/widgets/FLU`
23 | Authors: Jason Bryan
24 | License: GNU LGPL
25 |
26 | Location: `{src,include}/gui/widgets/Fl_Table`
27 | Authors: Greg Ercolano
28 | License: GNU LGPL
29 |
30 | Location: `include/util/bitset`
31 | Author: Anatoliy Kuznetsov
32 | License: MIT [`include/util/bitset/license.txt`]
33 |
34 | Location: `{src,include}/util/compress/bzip2`
35 | Author: Julian R Seward
36 | License: BSDish [`src/util/compress/bzip2/LICENSE`]
37 |
38 | Location: `{src,include}/util/compress/zlib`
39 | Authors: Jean-loup Gailly and Mark Adler
40 | License: BSDish [`include/util/compress/zlib/zlib.h`]
41 |
42 | Location: `{src,include}/util/regexp`
43 | Author: Philip Hazel
44 | License: BSDish [`src/util/regexp/doc/LICENCE.]
45 |
46 |
47 | Location: `{src,include}/misc/xmlwrapp`
48 | Author: Peter J Jones at al. [`src/misc/xmlwrapp/AUTHORS`]
49 | License: BSDish [`src/misc/xmlwrapp/LICENSE`]
50 |
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/_posts/2015-06-09-faq.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "FAQ"
5 | order: 6
6 | ---
7 |
8 | Q. **Our product makes use of the NCBI source code, and we did changes and additions to that version of the NCBI code to better fit it to our needs. Can we copyright the code, and how?**
9 |
10 | A. You can copyright only the changes or the additions you made to the NCBI source code. You should identify unambiguously those sections of the code that were modified, e.g. by commenting any changes you made in the code you distribute. Therefore, your license has to make clear to users that your product is a combination of code that is public domain within the U.S. (but may be subject to copyright by the U.S. in foreign countries) and code that has been created or modified by you.
11 |
12 | Q. **Can we (re)license all or part of the NCBI source code?**
13 |
14 | A. No, you cannot license or relicense the source code written by NCBI since you cannot claim any copyright in the software that was developed at NCBI as a 'government work' and consequently is in the public domain within the U.S.
15 |
16 |
17 |
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/_posts/2015-06-09-fuse.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | title: "The FUSE client"
5 | order: 2
6 | ---
7 | The FUSE client can download the BLAST databases listed in [available BLAST databases]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %}). The
8 | client is configured to download the most recent version of these BLAST
9 | databases at the time of the first search, but these BLAST databases will not
10 | be automatically updated as newer databases become available.
11 |
12 | The FUSE client downloads the BLAST database over the network, so the first
13 | BLAST search against a new database will be slow. The client caches the
14 | database on disk and subsequent searches will be faster.
15 | Or, terminate the existing instance and start a new one. The new instance will cache the latest data.
16 |
17 |
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/_posts/2015-06-09-intended-audience.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: intro
4 | title: "Intended Audience"
5 | order: 1
6 | ---
7 |
8 | The NCBI BLAST AMI will be useful to a variety of users. The requirements for
9 | using it and how easy it will be to set up will depend on the user's workflow
10 | and the level of expertise with setting up computing resources on a cloud
11 | service provider.
12 |
13 | For those without a background in computers, having familiarity with cloud
14 | services is helpful, but not mandatory, as the AWS Marketplace provides a
15 | 1-Click-Launch option and documentation on how to start/stop your instances.
16 | If you run into any difficulty, please feel free to email us at
17 | blast-help@ncbi.nlm.nih.gov so we can help you!
18 |
19 | A typical scenario would be to have one user in a group/team to register at a cloud
20 | provider, configure the instance, and handle payment for the running
21 | instance(s). Other members of the group/team can then use the instance through the
22 | [Common URL API]({{site.baseurl}}{% post_url 2015-06-09-api %}) or [webpage]({{site.baseurl}}{% post_url 2015-06-09-running-web-blast %})
23 | without their own cloud provider account. The Common URL API interface
24 | is ideal for users familiar with the BLAST URL API at the NCBI. Currently, the
25 | BLAST server image runs searches on only one instance. Many simultaneous users,
26 | could overload a single instance, to avoid this [monitor your instance](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/monitoring-system-instance-status-check.html).
27 |
28 | Please see the table below for specific examples:
29 |
30 | | Task/workflow | 1-click-start | Knowledge of ssh/scp/networking| Optimal data center region| Programmatic access via [Common URL API]({{site.baseurl}}{% post_url 2015-06-09-api %})|
31 | |---------------|---------------|---------------------------------|------------------------|--------------------|
32 | |BLAST against protein nr, swissprot, refseq_protein, pdbaa, or nucleotide nt, pdbnt, refseq_rna via web interface|Yes (1) |Limited (4)| us-east-1 (N. Virginia)| Not applicable|
33 | |BLAST your own/propietary sequence data (2,3) |Limited options|Required (4)|Closest to where your data is *stored*|Optional|
34 | |Third party application developers to run BLAST (3)|Limited options|Required (4)|Depends on user's workflow (see two rows above)|Likely required|
35 |
36 | ##### Foot notes
37 |
38 | 1. The 1-Click-Launch option is configured by default to start a `m4.10xlarge` instance (40 vCPUs, 160 GB RAM, EBS volumes, $2/hr), which is large enough (as of 06/08/2018) to run searches against the nr and nt BLAST databases and store the results in the instance's local disk.
39 | 2. For those users with proprietary sequence data, you can convert that sequence data into BLAST databases and [upload the resulting BLAST databases to a running instance]({{site.baseurl}}{% post_url 2015-06-09-updating-blastdbs %}).
40 | 3. Please be sure to [choose an appropriately sized instance]({{site.baseurl}}{% post_url 2015-06-09-choosing-instance %}) for your workload.
41 | 4. Please see [setting up remote access]({{site.baseurl}}{% post_url 2015-06-09-setting-up-remote-access %}).
42 |
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/_posts/2015-06-09-logging-in.md:
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1 | ---
2 | layout: page
3 | category: usage
4 | title: "Logging into an instance"
5 | order: 4
6 | ---
7 |
8 | The BLAST server image uses Ubuntu Linux, so you should use the user name `ubuntu`
9 | rather than `root`, `centos`, `ec2-user`, or your own username for the ssh
10 | connection. On Windows you can use [putty](https://www.putty.org/); in Linux and macOS you usually `ssh` is
11 | available by default.
12 |
13 |
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/_posts/2015-06-09-motivation.md:
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1 | ---
2 | layout: page
3 | category: intro
4 | title: "Motivation"
5 | order: 0
6 | ---
7 |
8 | Basic Local Alignment Search Tool (BLAST) is a popular sequence similarity
9 | search tool. The National Center for Biotechnology Information (NCBI) maintains
10 | a public BLAST server at
11 | [blast.ncbi.nlm.nih.gov](https://blast.ncbi.nlm.nih.gov). The NCBI BLAST server
12 | is intended mainly for interactive use, with the expectation that users will
13 | perform a moderate number of searches (i.e., 10-20) per day.
14 |
15 | Some users have
16 | many more searches to perform than can be accommodated at the NCBI site. For
17 | such batch users, the NCBI offers the stand-alone BLAST+ package that can be
18 | run on local hardware. Running the stand-alone package requires that the user
19 | have access to sufficient compute resources (e.g., a local cluster) as well as
20 | some degree of familiarity with IT issues and command-line applications.
21 |
22 | Additionally, some users do not need to perform a large number of searches on a
23 | regular basis, but may need to do so occasionally. Some users have proprietary
24 | sequence data to search and cannot use the NCBI BLAST web site.
25 | A cloud provider may offer an acceptable solution for these scenarios.
26 |
27 |
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/_posts/2015-06-09-other-ncbi-blastdbs.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Additional NCBI BLAST databases"
5 | order: 3
6 | ---
7 |
8 | Users may want to install additional BLAST databases from the NCBI using the
9 | `update_blastdb.pl` program. First, [log in to your running
10 | instance via ssh]({{site.baseurl}}{% post_url 2015-06-09-logging-in %}) and run the
11 | commands below :
12 |
13 | cd /blast/blastdb_custom
14 | update_blastdb.pl --decompress --passive
15 |
16 |
17 | The table below shows some of the available BLAST databases via this method (subject to change without notice). To see all available BLAST databases, please run the command `update_blastdb.pl --showall --passive`.
18 |
19 | |Name |Title |Type|
20 | |--------|---------------------|----|
21 | |16SMicrobial |16S ribosomal RNA sequences from bacteria and archaea (RefSeq)|DNA |
22 | |landmark |The [landmark database](https://blast.ncbi.nlm.nih.gov/smartblast/smartBlast.cgi?CMD=Web&PAGE_TYPE=BlastDocs) includes proteomes from 27 genomes spanning a wide taxonomic range |Protein|
23 | |human_genomic|Assembled human chromosomes from Reference and Genbank for various individuals, along with their scaffold components.|DNA|
24 | |refseqgene|Genomic sequences for selected genes records from NCBI RefSeq project (NG accessioned), containing additional up- and downstream sequences beyond the transcribed region.|DNA|
25 | |vector|A database contains common vector sequences found in the GenBank/EMBL/DDBJ.|DNA|
26 | |pataa|Protein sequences from patents as supplied by USPTO. Its entries are EXCLUDED from the nr database.|Protein|
27 | |patnt|The patent nucleotide sequence database contains entries from USPTO through GenBank or from EU/Japan Patent Agencies through EMBL/DDBJ. Entries are EXCLUDED from the nt database.|DNA|
28 | |tsa_nr|Protein sequences from annotated on the transcriptome shotgun assembly. Its entries are EXCLUDED from the nr database.|Protein|
29 | |tsa_nt|A database with earlier non-project based Transcriptome Sequence Assembly entries. Entries are EXCLUDED from the nt database.|DNA|
30 | |env_nr|Protein sequences from large environmental sequencing projects, e.g., Sargasso Sea, Acid Mine Drainage. Its entries are EXCLUDED from the nr database.|Protein|
31 | |env_nt|Nucleotide sequences from large environmental sequence projects, such as Sargasso Sea and Acid Mine Drainage. Its entries are EXCLUDED from the nt database.|DNA|
32 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-overview.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: intro
4 | title: "Overview"
5 | order: 2
6 | ---
7 |
8 | The NCBI provides a BLAST server image at Amazon Web Services
9 | (AWS). The BLAST server image includes a web application that provides
10 | a simplified BLAST search web page and supports the [NCBI-BLAST Common URL API]({{ site.baseurl }}{% post_url 2015-06-09-api %}),
11 | the BLAST+ applications,
12 | and a "FUSE" client that can cache databases from the NCBI (during the first search).
13 | The instance runs an HTTP server for the remote BLAST searches. The FUSE client can download
14 | a limited set of databases (see [the FUSE client]({{ site.baseurl }}{% post_url 2015-06-09-fuse %})).
15 | NCBI does not not charge for use of the software, but any instances will
16 | incur the cloud provider's charges.
17 |
18 | * The AWS Amazon Machine Image (AMI) can be run directly via the [AWS
19 | Marketplace](https://aws.amazon.com/marketplace/pp/B00N44P7L6).
20 |
21 | The BLAST server image supports three different search methods:
22 |
23 | 1. Users can ssh into the instance and [run stand-alone BLAST+ at the
24 | command-line]({{ site.baseurl }}{% post_url 2015-06-09-running-blast %}).
25 | 1. The instance has a [simple webpage for search submission]({{ site.baseurl }}{% post_url 2015-06-09-running-web-blast %}).
26 | 1. The instance supports the [NCBI-BLAST Common URL API interface]({{ site.baseurl }}{% post_url 2015-06-09-api %}).
27 |
28 | The latter two methods are remote searches that return a "Request ID" and **require** [authentication]({{ site.baseurl }}{% post_url 2015-06-09-authentication %}).
29 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-pre-cache-blastdbs.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Pre-caching BLAST databases"
5 | order: 5
6 | ---
7 |
8 | One way to speed-up BLAST is to pre-load the BLAST database files into main
9 | memory. In the case of BLAST databases retrieved by `remote-fuser`, this
10 | pre-caching will trigger download of the database files on to local disk.
11 |
12 | This can be achieved by running the command below on your instance:
13 |
14 | /usr/bin/cat ${PATH_TO_BLAST_DATABASE_FILES} >/dev/null
15 |
16 | For instance, to pre-cache the nucleotide nt database files, please run the command:
17 |
18 | /usr/bin/ls /blast/blastdb/nt.*n{in,sq} | /usr/bin/xargs -P$(/usr/bin/grep -c ^processor /proc/cpuinfo) -t -I{} /usr/bin/cat {} >/dev/null
19 |
20 | The command above sends the output of the `ls` command to `xargs` to execute
21 | the `cat` command on multiple files in parallel.
22 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-running-blast.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Running BLAST+"
5 | order: 5
6 | ---
7 | The BLAST server image already has the BLAST+ applications ([publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803857/), [quick start](https://www.ncbi.nlm.nih.gov/books/NBK279680/), [cookbook](https://www.ncbi.nlm.nih.gov/books/NBK279696/)) installed and will
8 | retrieve the databases listed [here]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %}) on demand (i.e.: when the first BLAST search of that BLAST database occurs).
9 | Users familiar with command line interfaces can run the BLAST+ applications directly on their
10 | instance by [logging on via ssh]({{site.baseurl}}{% post_url 2015-06-09-logging-in %}) (requires [setting up remote access]({{site.baseurl}}{% post_url 2015-06-09-setting-up-remote-access %}))
11 | and issuing commands at the terminal prompt.
12 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-running-web-blast.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Running Web BLAST"
5 | order: 3
6 | ---
7 | To run WebBLAST on the instance you [started at AWS]({{ site.baseurl }}{% post_url 2015-06-09-starting-instance %}), simply point your web browser at the Public DNS of your instance with the suffix `cgi-bin/blast.cgi`:
8 |
9 | **Note**: You will need to [authenticate]({{ site.baseurl }}{% post_url 2015-06-09-authentication %}) the first time you access this URL.
10 |
11 | 
12 |
13 |
14 | By clicking on the 'Recent Results' tab near of the top of the page you will be able to see the BLAST searches that have run on this instance, their status, and access their results:
15 |
16 | 
17 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-setting-up-remote-access.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: conf
4 | title: "Setting up remote access"
5 | order: 1
6 | ---
7 |
8 | If you wish to allow BLAST searches via a web browser, then you will need to enable HTTP access
9 | when you configure your instance *and* provide [authentication]({{ site.baseurl }}{% post_url 2015-06-09-authentication %})
10 | (please see [Running Web BLAST]({{ site.baseurl }}{% post_url 2015-06-09-running-web-blast %}) and
11 | [Common URL API]({{ site.baseurl }}{% post_url 2015-06-09-api %})). By default,
12 | the AMI enables these, so please read on.
13 |
14 | In allowing HTTP access, it is very important that you
15 | configure your security group/network firewall properly. If this is not restricted appropriately, anyone
16 | with knowledge of your public DNS may perform remote searches on your instance,
17 | see all the BLAST results for remote searches or delete the results. If
18 | possible, you should configure the security group/network firewall of your instance to
19 | allow HTTP access only from a specific set of IP's (e.g. your lab's network). You should
20 | also only share the public DNS of your instance with people who have your
21 | permission to use it.
22 |
23 | As a security precaution, the BLAST AMI by default blocks all ports but 22 (for ssh) and 80 (for HTTP access).
24 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-starting-instance.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Starting an instance"
5 | order: 0
6 | ---
7 |
8 | An account is required with Amazon Web Services (AWS). As cloud providers rapidly change their product offerings, please consult their cloud documentation first.
9 |
10 | 1. Start at the [NCBI BLAST home page](https://blast.ncbi.nlm.nih.gov) and click on "Use BLAST in the cloud".
11 | 
12 |
13 | 2. Click on the [AWS marketplace link](https://aws.amazon.com/marketplace/pp/B00N44P7L6).
14 | 
15 |
16 | 3. Click on **'Continue to Subscribe'**. (What does it mean to [subscribe](https://aws.amazon.com/marketplace/help/200799470)?)
17 | 
18 |
19 | 4. Login with your AWS credentials (requires sign up and credit card information).
20 | 
21 |
22 | 5. Select **'Launch with 1-click'** yellow button (circled in red, see 5a below).
23 | The 1-Click-Launch option is configured by default to start a `m4.10xlarge` instance (40 vCPUs, 160 GB RAM, EBS volumes, $2/hr), which is large enough (as of 06/08/2018) to run searches against the nr and nt BLAST databases and store the results in the instance's local disk.
24 | **NOTE**: The following two screenshots may not reflect the most recent web interface for the AWS Marketplace.
25 | Recommendations:
26 | * Please use an instance with EBS volumes if you intend to stop or reboot the instance.
27 | * Start the instance in the `us-east-1` region, as it is closest to NCBI and the BLAST database downloads will be the fastest.
28 | 5a
29 | Machine type can be changed using the area highlighted in green (see 5b below and adjusted hourly price).
30 | 5b
31 | **NOTE**: If you want to [login to the instance via ssh]({{site.baseurl}}{% post_url 2015-06-09-logging-in %}), please be sure to set the proper Key Pair and open the required ports to enable access. If this is not needed, no worries! You can still access the web application via the web browser.
32 |
33 | 6. A confirmation page will appear. To get the URL of your instance, follow the "Console" link (highlighted in red below). This is also accessible via the [AWS console](https://console.aws.amazon.com/ec2/).
34 | 
35 |
36 | 7. In the AWS console, follow the link to **'Running Instances'**.
37 | 
38 |
39 | 8. Identify your running instance. One way of achieving this is as follows:
40 | * Sort the instances by descending launch time (newest first); since yours is likely to be at/near the top.
41 | * Copy the public DNS for the machine _and_ the instance ID.
42 | 
43 |
44 | 9. Paste the public DNS into your web browser.
45 | 
46 |
47 | 10. Click on **'BLAST QUERY'** and in the 'Sign in' window enter: **User name** - 'blast' and **Password** - (instance ID from the previous step):
48 | 
49 |
50 | 11. You are all set! Run BLAST to your heart's content :)
51 | 
52 |
53 |
54 |
55 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-stopping-instance.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Stopping an instance"
5 | order: 1
6 | ---
7 |
8 | **NOTE 1**: _Stoppage_ allows the instance to be stopped and re-started at a later time. Any previously computed BLAST results will still be available once the instance is re-started. AWS will only charge a small fee for storage of the data in an EBS volume.
9 |
10 | **NOTE 2**: Stopping an instance will **delete** any of the [available BLAST databases]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %}) that were already downloaded. When the instance is re-started, the [BLAST databases]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %}) will be downloaded on demand.
11 |
12 | **NOTE 3**: _Termination_ of instance is permanent, all data stored in the instance is lost forever.
13 |
14 | **WARNING**: You may want to download your BLAST results before **terminating** the instance, as once this is done, all the contents of the instance will be lost.
15 |
16 | 1. Login to the [AWS console](https://console.aws.amazon.com/ec2).
17 |
18 | 2. Identify the instance you would like stop **OR** terminate (tip: use the instance ID as a means to filter the listing of running instances).
19 | 
20 |
21 | 3. Click on 'Actions -> Instance State -> Stop' **OR** 'Actions -> Instance State -> Terminate'.
22 | 
23 |
24 | 4. Confirm the Stop (4a) **OR** termination(4b).
25 | 4a
26 | 4b
27 |
28 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-troubleshooting.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: usage
4 | title: "Troubleshooting"
5 | order: 7
6 | ---
7 |
8 | If you have problems that are not addressed below, please do not hesitate to reach out to NCBI for help: blast-help@ncbi.nlm.nih.gov.
9 |
10 | ### The initial BLAST search takes too long
11 |
12 | The BLAST databases are fetched from the NCBI (located in the east coast of North America), so if your instance is running in a region that is geographically far from NCBI, you will likely experience lengthy BLAST download times. Please see [how to choose a region]({{site.baseurl}}{% post_url 2015-06-09-data-center-location %}).
13 |
14 | ### BLAST takes too long
15 |
16 | To run BLAST optimally, the BLAST database should fit in the host's main memory (i.e.: RAM). Please see [how to choose an instance]({{site.baseurl}}{% post_url 2015-06-09-choosing-instance %}).
17 |
18 |
19 |
20 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-updating-blastdbs.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: blastdb
4 | title: "Updating BLAST databases"
5 | order: 1
6 | ---
7 |
8 | There are two ways of updating the [BLAST databases]({{site.baseurl}}{% post_url 2015-06-09-available-blastdbs %})
9 | that come installed by default in the BLAST AMI:
10 |
11 |
12 | #### 1. Restart remote-fuser
13 | [Login to the instance]({{site.baseurl}}{% post_url 2015-06-09-logging-in %}) and issue the following commands *when there are no BLAST searches running on your instance*:
14 |
15 | /sbin/remote-fuser-ctl.pl --stop
16 | /sbin/remote-fuser-ctl.pl --start
17 |
18 | This will discard the already downloaded BLAST databases and switch to the latest available BLAST databases from NCBI.
19 |
20 | An optional optimization step would be to [pre-cache the BLAST
21 | databases]({{site.baseurl}}{% post_url 2015-06-09-pre-cache-blastdbs %}).
22 |
23 | #### 2. Restart the instance
24 | [Stop]({{site.baseurl}}{% post_url 2015-06-09-stopping-instance %}) and [re-start]({{site.baseurl}}{% post_url 2015-06-09-starting-instance %}) the instance.
25 |
--------------------------------------------------------------------------------
/_posts/2015-06-09-using-url-api.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | category: dev
4 | title: "Using the Common URL API"
5 | order: 1
6 | ---
7 | This page describes how to use the [NCBI-BLAST Common URL API]({{ site.baseurl }}{% post_url 2015-06-09-api %}) to run remote BLAST searches. These instructions assume you are running searches at a cloud provider, but minor modifications
8 | allow you to run searches at the NCBI web server. A note at the bottom of this page provides information on searches at the NCBI.
9 |
10 | To run a search, you should:
11 |
12 | 1. Launch a BLAST instance. The security group must allow access through HTTP.
13 | If possible, restrict the allowed IP's for HTTP so as to include only those
14 | of the intended users. See [setting up remote access]({{site.baseurl}}{% post_url 2015-06-09-setting-up-remote-access %}) and your cloud provider's documentation. The examples
15 | on this page assume Amazon Web Services (AWS).
16 |
17 | 1. Once the instance has launched, obtain the Public DNS from your cloud provider.
18 | For AWS, the Public DNS will look like:
19 | `http://ec2-54-82-43-97.compute-1.amazonaws.com` though the exact numbers and letters
20 | will be depend upon your instance.
21 |
22 | 1. Launch a search using your Public DNS plus cgi-bin/blast.cgi. You will need to
23 | [authenticate]({{ site.baseurl }}{% post_url 2015-06-09-authentication %}) before submitting a search.
24 | For the example Public DNS given above, a URL to search the sequence of accession
25 | u00001 against nt would be:
26 | `http://ec2-54-82-43-97.compute-1.amazonaws.com/cgi-bin/blast.cgi?QUERY=u00001&DATABASE=nt&PROGRAM=blastn&CMD=Put`
27 |
28 | 1. The server will respond with HTML containing a `QBlastInfo` block. The QBlastInfo block will contain
29 | a RID ("Request ID") that can be used to retrieve results as well as a RTOE that is an estimated time in seconds
30 | until the search is completed. An example QBlastInfo block is:
31 |
32 | ```
33 |
38 | ```
39 |
40 | 1. You may check the status of the search by invoking blast.cgi with the parameters `CMD=Get`,
41 | `FORMAT_OBJECT=SearchInfo`, and `RID=VALUE`, where `VALUE` is the `RID` returned by
42 | the server. The server will respond with a page containing a `QBlastInfo`
43 | block with the status set as one of `WAITING`, `UNKNOWN`, or `READY`.
44 |
45 | 1. Once the search is finished, you may retrieve results by invoking blast.cgi
46 | with the parameters `CMD=GET` and `RID=VALUE`, where `VALUE` is the `RID` the system
47 | returned. An example would be "CMD=Get&RID=6NTRF1YLO8". You may also specify
48 | the report type (e.g, add `FORMAT_TYPE=Text`).
49 |
50 | **Note**: If you have not restricted your security group, anybody
51 | with knowledge of your public DNS can use `CMD=DisplayRIDs` to see all remote
52 | searches available on the system.
53 |
54 | **Note**: The BLAST server at the NCBI supports the same URL API. At the NCBI, you should
55 | use the URL https://blast.ncbi.nlm.nih.gov/Blast.cgi but follow the same basic procedure. Naturally, you do not need to launch an instance first. Note that only HTTPS is supported at the NCBI server after 09/30/2016. The NCBI BLAST
56 | server is a shared resource and usage restrictions may apply. See information
57 | [here](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo).
58 |
--------------------------------------------------------------------------------
/bin/jekyll-page:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env ruby
2 |
3 | require 'date'
4 | require 'optparse'
5 |
6 | options = {
7 | # Expects to be in the bin/ sub-directory by default
8 | :path => File.dirname(File.dirname(__FILE__))
9 | }
10 |
11 | parser = OptionParser.new do |opt|
12 | opt.banner = 'usage: jekyll-page TITLE CATEGORY [FILENAME] [OPTIONS]'
13 | opt.separator ''
14 | opt.separator 'Options'
15 | opt.on('-e', '--edit', 'Edit the page') do |edit|
16 | options[:edit] = true
17 | end
18 | opt.on('-l', '--link', 'Relink pages') do |link|
19 | options[:link] = true
20 | end
21 | opt.on('-p PATH', '--path PATH', String, 'Path to project root') do |path|
22 | options[:path] = path
23 | end
24 | opt.separator ''
25 | end
26 |
27 | parser.parse!
28 |
29 | title = ARGV[0]
30 | category = ARGV[1]
31 | filename = ARGV[2]
32 |
33 | # Resolve any relative links
34 | BASE_DIR = File.expand_path(options[:path])
35 | POSTS_DIR = "#{BASE_DIR}/_posts"
36 | PAGES_DIR = "#{BASE_DIR}/_pages"
37 |
38 | # Ensure the _posts directory exists (we are in the correct directory)
39 | if not Dir.exists?(POSTS_DIR)
40 | puts "#{POSTS_DIR} directory does not exists"
41 | exit
42 | end
43 |
44 | # Create _pages directory if it doesn't exist
45 | if not Dir.exists?(PAGES_DIR)
46 | Dir.mkdir(PAGES_DIR)
47 | end
48 |
49 | if options[:link]
50 | Dir.foreach(POSTS_DIR) do |name|
51 | next if name[0] == '.'
52 | nodate = name[/\d{4}-\d{2}-\d{2}-(?.*)/, 'rest']
53 | if File.symlink?("#{PAGES_DIR}/#{nodate}")
54 | File.delete("#{PAGES_DIR}/#{nodate}")
55 | end
56 | abspath = File.absolute_path("#{POSTS_DIR}/#{name}")
57 | File.symlink(abspath, "#{PAGES_DIR}/#{nodate}")
58 | end
59 | end
60 |
61 | if not title or not category
62 | # This flag can be used by itself, exit silently if no arguments
63 | # are defined
64 | if not options[:link]
65 | puts parser
66 | end
67 | exit
68 | end
69 |
70 | if not filename
71 | filename = title.downcase.gsub(/[^a-z0-9\s]/, '').gsub(/\s+/, '-')
72 | end
73 |
74 | today=Date.today().strftime('%F')
75 | now=DateTime.now().strftime('%F %T')
76 |
77 | filepath = "#{POSTS_DIR}/#{today}-#{filename}.md"
78 | symlink = "#{PAGES_DIR}/#{filename}.md"
79 |
80 | if File.exists?(filepath)
81 | puts "File #{filepath} already exists"
82 | exit
83 | end
84 |
85 | content = < .page-header:first-child {
38 | margin-top: 0;
39 | }
40 |
41 | #content > .page-header:first-child h2 {
42 | margin-top: 0;
43 | }
44 |
45 |
46 | #navigation {
47 | font-size: 0.9em;
48 | }
49 |
50 | #navigation li a {
51 | padding-left: 10px;
52 | padding-right: 10px;
53 | }
54 |
55 | #navigation .nav-header {
56 | padding-left: 0;
57 | padding-right: 0;
58 | }
59 |
60 | /* Copied from for-ie-only.css from pubmed-labs */
61 |
62 | table {
63 | border-collapse: collapse;
64 | border-spacing: 0;
65 | margin-bottom: 1.375em;
66 | font-size: 0.875em;
67 | }
68 |
69 | .table-code code {
70 | background-color: #ffffff;
71 | border: 1px solid #e3e4e5;
72 | border-radius: 0.250em;
73 | overflow-x: auto;
74 | padding: 0.125em 0.250em;
75 | white-space: pre-wrap;
76 | }
77 |
78 | th {
79 | text-align: left;
80 | font-family: "Avenir Next Demi", Arial, sans-serif;
81 | /*background-color: #dbedd4;*/
82 | background-color: #a2e4ee;
83 | }
84 |
85 | tr, th, td {
86 | padding: 10px 15px;
87 | line-height: 1.5em;
88 | }
89 |
90 | td:code {
91 | background-color: transparent;
92 | white-space: nowrap;
93 | }
94 |
95 | tr:nth-child(even) {
96 | background-color: #F1F2F2;
97 | }
98 |
99 | tr:nth-child(odd) {
100 | background-color: #F8F8F8;
101 | }
102 |
103 | table.fullwidth tr:nth-child(odd) {
104 | background-color: transparent;
105 | }
106 |
107 | table.fullwidth tr:nth-child(even) {
108 | background-color: transparent;
109 | }
110 |
111 | .field-table td:nth-child(1) {
112 | }
113 |
114 | .field-table {
115 | width: 100%;
116 | table-layout: fixed;
117 | }
118 |
119 | .field-table code {
120 | background-color: #ffffff;
121 | border: 1px solid #e3e4e5;
122 | border-radius: 0.250em;
123 | overflow-x: auto;
124 | padding: 0.125em 0.250em;
125 | white-space: nowrap;
126 | }
127 |
--------------------------------------------------------------------------------
/css/syntax.css:
--------------------------------------------------------------------------------
1 | .highlight .hll { background-color: #ffffcc }
2 | .highlight { background: #ffffff; }
3 | .highlight .c { color: #888888 } /* Comment */
4 | .highlight .err { color: #a61717; background-color: #e3d2d2 } /* Error */
5 | .highlight .k { color: #008800; font-weight: bold } /* Keyword */
6 | .highlight .cm { color: #888888 } /* Comment.Multiline */
7 | .highlight .cp { color: #cc0000; font-weight: bold } /* Comment.Preproc */
8 | .highlight .c1 { color: #888888 } /* Comment.Single */
9 | .highlight .cs { color: #cc0000; font-weight: bold; background-color: #fff0f0 } /* Comment.Special */
10 | .highlight .gd { color: #000000; background-color: #ffdddd } /* Generic.Deleted */
11 | .highlight .ge { font-style: italic } /* Generic.Emph */
12 | .highlight .gr { color: #aa0000 } /* Generic.Error */
13 | .highlight .gh { color: #333333 } /* Generic.Heading */
14 | .highlight .gi { color: #000000; background-color: #ddffdd } /* Generic.Inserted */
15 | .highlight .go { color: #888888 } /* Generic.Output */
16 | .highlight .gp { color: #555555 } /* Generic.Prompt */
17 | .highlight .gs { font-weight: bold } /* Generic.Strong */
18 | .highlight .gu { color: #666666 } /* Generic.Subheading */
19 | .highlight .gt { color: #aa0000 } /* Generic.Traceback */
20 | .highlight .kc { color: #008800; font-weight: bold } /* Keyword.Constant */
21 | .highlight .kd { color: #008800; font-weight: bold } /* Keyword.Declaration */
22 | .highlight .kn { color: #008800; font-weight: bold } /* Keyword.Namespace */
23 | .highlight .kp { color: #008800 } /* Keyword.Pseudo */
24 | .highlight .kr { color: #008800; font-weight: bold } /* Keyword.Reserved */
25 | .highlight .kt { color: #888888; font-weight: bold } /* Keyword.Type */
26 | .highlight .m { color: #0000DD; font-weight: bold } /* Literal.Number */
27 | .highlight .s { color: #dd2200; background-color: #fff0f0 } /* Literal.String */
28 | .highlight .na { color: #336699 } /* Name.Attribute */
29 | .highlight .nb { color: #003388 } /* Name.Builtin */
30 | .highlight .nc { color: #bb0066; font-weight: bold } /* Name.Class */
31 | .highlight .no { color: #003366; font-weight: bold } /* Name.Constant */
32 | .highlight .nd { color: #555555 } /* Name.Decorator */
33 | .highlight .ne { color: #bb0066; font-weight: bold } /* Name.Exception */
34 | .highlight .nf { color: #0066bb; font-weight: bold } /* Name.Function */
35 | .highlight .nl { color: #336699; font-style: italic } /* Name.Label */
36 | .highlight .nn { color: #bb0066; font-weight: bold } /* Name.Namespace */
37 | .highlight .py { color: #336699; font-weight: bold } /* Name.Property */
38 | .highlight .nt { color: #bb0066; font-weight: bold } /* Name.Tag */
39 | .highlight .nv { color: #336699 } /* Name.Variable */
40 | .highlight .ow { color: #008800 } /* Operator.Word */
41 | .highlight .w { color: #bbbbbb } /* Text.Whitespace */
42 | .highlight .mf { color: #0000DD; font-weight: bold } /* Literal.Number.Float */
43 | .highlight .mh { color: #0000DD; font-weight: bold } /* Literal.Number.Hex */
44 | .highlight .mi { color: #0000DD; font-weight: bold } /* Literal.Number.Integer */
45 | .highlight .mo { color: #0000DD; font-weight: bold } /* Literal.Number.Oct */
46 | .highlight .sb { color: #dd2200; background-color: #fff0f0 } /* Literal.String.Backtick */
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50 | .highlight .se { color: #0044dd; background-color: #fff0f0 } /* Literal.String.Escape */
51 | .highlight .sh { color: #dd2200; background-color: #fff0f0 } /* Literal.String.Heredoc */
52 | .highlight .si { color: #3333bb; background-color: #fff0f0 } /* Literal.String.Interpol */
53 | .highlight .sx { color: #22bb22; background-color: #f0fff0 } /* Literal.String.Other */
54 | .highlight .sr { color: #008800; background-color: #fff0ff } /* Literal.String.Regex */
55 | .highlight .s1 { color: #dd2200; background-color: #fff0f0 } /* Literal.String.Single */
56 | .highlight .ss { color: #aa6600; background-color: #fff0f0 } /* Literal.String.Symbol */
57 | .highlight .bp { color: #003388 } /* Name.Builtin.Pseudo */
58 | .highlight .vc { color: #336699 } /* Name.Variable.Class */
59 | .highlight .vg { color: #dd7700 } /* Name.Variable.Global */
60 | .highlight .vi { color: #3333bb } /* Name.Variable.Instance */
61 | .highlight .il { color: #0000DD; font-weight: bold } /* Literal.Number.Integer.Long */
62 |
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/index.md:
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1 | ---
2 | layout: page
3 | title: "NCBI BLAST Cloud Documentation"
4 | ---
5 |
6 | **The BLAST AMI has been deprecated and is no longer supported. Please see our Cloud [documentation](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast) for other options.**
7 |
8 |
9 |
10 |
11 | _Do you have difficulties running a large number of BLAST searches?
12 | Do you have proprietary sequence data to BLAST and cannot use the NCBI BLAST web site?
13 | Do you want to avoid the work to set up and maintain the (command-line) BLAST+ applications?_
14 |
15 | If you answered yes to any of these questions, running your own BLAST server on the cloud maybe your best solution.
16 |
17 |
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