<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/2791?offset=210 https://bioinformaticsonline.com/news/view/40589/new-layout-for-blast-ftp-database-site Tue, 21 Jan 2020 11:57:11 -0600 https://bioinformaticsonline.com/news/view/40589/new-layout-for-blast-ftp-database-site <![CDATA[New Layout for BLAST ftp Database Site]]> As announced previously, the new default database version for BLAST+ is dbV5.  To complete this transition, the ftp database site will be updated to support this change.  We expect this change to happen around February 4th, please adjust your scripts or procedures accordingly.

Here is a list of what is changing:

  1. All databases at the root level will be dbV5.
  2. The dbV5 file naming,  “_v5” will be removed. Databases with  no “_vX” descriptor will be dbV5.
  3. dbV4 tarballs will be renamed with "_v4", files included in tarball will not be renamed.
  4. dbV4 databases will be moved to a v4 subdirectory.
  5. As of 1/13/20 the Cloud directory will be frozen with no more new entries.
  6. The will be no more updates to dbV4 databases.
  7. The FASTA directory will contain nr, nt, swissprot, and pdbaa files.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

]]> Jit https://bioinformaticsonline.com/blog/view/43424/rest-api Mon, 04 Oct 2021 12:46:40 -0500 https://bioinformaticsonline.com/blog/view/43424/rest-api <![CDATA[REST API]]> REST API

The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language
Download
Requirements
Perl psiblast.pl LWP and XML::Simple

Python

psiblast.py

 xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

]]> Neel https://bioinformaticsonline.com/bookmarks/view/2727/download-mutliple-fasta-file-from-ncbi-in-one-go Wed, 21 Aug 2013 08:13:30 -0500 https://bioinformaticsonline.com/bookmarks/view/2727/download-mutliple-fasta-file-from-ncbi-in-one-go <![CDATA[Download mutliple fasta file from NCBI in one GO!!]]> if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs .

Alternatively, use one liner perl script:

perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta

where GIs.txt contains a list of GIs or accession IDs.

(from :http://edwards.sdsu.edu/labsite/index.php/robert?start=5)

Address of the bookmark: http://edwards.sdsu.edu/labsite/index.php/robert/380-ncbi-sequence-or-fasta-batch-download-using-entrez

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/43620/ncbi-datasets-cli-quickstart-command-line-tools Tue, 07 Dec 2021 02:51:26 -0600 https://bioinformaticsonline.com/bookmarks/view/43620/ncbi-datasets-cli-quickstart-command-line-tools <![CDATA[ncbi-datasets-cli -- Quickstart: command line tools !]]> Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

 https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

]]> Jit https://bioinformaticsonline.com/videolist/watch/11195/ncbi-gene-screencast Fri, 30 May 2014 06:21:18 -0500 https://bioinformaticsonline.com/videolist/watch/11195/ncbi-gene-screencast <![CDATA[NCBI Gene Screencast]]> A short walkthrough of the NCBI Gene page]]> https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 Thu, 12 May 2016 13:49:41 -0500 https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 <![CDATA[Release Notes for Genome Workbench 2.10.5]]> New Features in latest release

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)
]]> Jit https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line Wed, 19 Oct 2016 08:06:24 -0500 https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line <![CDATA[Entrez Direct: E-utilities on the UNIX Command Line]]> Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

]]> Anjana