BOL: Related items

BLAST+ 2.10.0 released

Jit — Wed, 18 Dec 2019 20:44:11 -0600

The BLAST+ 2.10.0 release is now available from at FTP site. The new version offers the following improvements:

updated composition-based statistics for protein-protein (including translated BLAST) comparisons to provide stable results when you request fewer than the default number of results
an experimental Adaptive Composition Based Statistics option that increases the likelihood of finding novel results. To enable this option set the environment variable ADAPTIVE_CBS to 1. We welcome your feedback on this new option.

See the release notes for details on more improvements and bug fixes with this release.

BLAST+ is also available in docker, please read more for details.

The new version fully supports the version 5 (v5) databases with built in taxonomy and other improvements. For more information on v5 databases (download), see the previous NCBI Insights article and the recording of our webinar. If you are still using the older version 4 (v4) databases, we recommend you begin using the v5 version as soon as possible. We will discontinue updates to the older v4 databases in early 2020.

BLAST+ Team

NCBI BLAST have added new columns to the Descriptions

Neel — Tue, 01 Dec 2020 09:56:07 -0600

NCBI BLAST have added new columns to the Descriptions Table for web BLAST output. The new columns are Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click 'Select columns' or 'Manage columns' to add or remove columns from the display Your preferences will be saved for your next visit to BLAST, and when you download your results, whatever columns you have displayed will be saved. See the NCBI Insights post (https://go.usa.gov/x7fPE) for more details.

Webinar: BLAST in the Cloud

Mon, 15 Sep 2014 17:29:32 -0500

Presented July 30, 2014 and covering: an NCBI BLAST AMI at Amazon Web Services; introduction to AWS and setting up an instance; running command line BLAST and using the BLAST URL API via the AMI; and answers to attendee questions.

The Breeding API (BrAPI) project

BioStar — Wed, 06 Jan 2021 19:51:17 -0600

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Address of the bookmark: https://brapi.org/

Demo 4: Using BLAST/BLAT in Ensembl

Tue, 10 Sep 2013 11:54:03 -0500

We demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.

Genome Workbench 2.10.7

Gudiya Pal — Fri, 01 Jul 2016 12:09:59 -0500

Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

BLAST Tool: added support for local custom BLAST databases
Graphical Sequence View: added log scaling option for graph tracks
Generic Table View: new tutorial added

Bug Fixes and Improvements

Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
Tree View: layout updated to better accommodate nodes of different sizes
Table Import Dialog (MacOS): fixed issue with table visibility
Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
Graphical Sequence View: fixed protein coloration methods
Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
Search View: ORF Finder – fixed incorrect protein lengths
Fixed bug with not opening project file (.gbp) on a click
Fixed issues in GVF import
Fixed BLAST Search tool against NCBI databases not working
Fixed tblastn (protein BLAST) not working in standalone mode
Fixed GTF export failure

DIAMOND

Jit — Thu, 27 Apr 2017 04:21:54 -0500

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

BLAST nr version 5 database, (nr_v5)

Jit — Fri, 23 Aug 2019 11:35:35 -0500

NCBI have made changes the nr version 5 database, (nr_v5), to facilitate better search results and improved performance by reducing the number of redundant titles in the nr_v5 database used by webBLAST, which is also available for BLAST+ users.

The changes in nr preserve the taxonomic diversity of the entries in the database while reducing the number of titles for identical sequences. GenPept accessions are still accessible via www.ncbi.nlm.nih.gov/protein/$GENBANK_ACCESSION or the IPG website https://www.ncbi.nlm.nih.gov/ipg/.

The "Identical Proteins" link in the alignments section of the webBLAST results takes you to a full list of all accessions associated with a sequence.

For BLAST+ users downloading nr_v5: the database is now approximately 50% smaller, resulting in faster downloads and BLAST searches, and smaller disk space requirements. The database is downloadable at: ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/

For BLAST+ there is a cleanup script to help you manage the transition to this smaller database. The script removes unused database volumes: ftp://ftp.ncbi.nlm.nih.gov/blast/temp/cleanup-blastdb-volumes.py

Here are the new rules on how we keep titles in nr_v5:

1. We keep all refseq, swissprot, pir and PDB titles.

2. We keep any GenPept titles with a TAXID that has not already been seen in the record.

3. We keep at least five GenPept titles regardless of whether the TAXIDS have been seen before or not in this record.

Primer BLAST !

BioStar — Tue, 28 Apr 2020 00:28:49 -0500

BLAST team added a new feature (Max 3' match), shown in Figure 1, to Primer-BLAST that limits the length of 3' exon matches when designing exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in expression assays. See the NCBI Insights post (https://go.usa.gov/xvUT4) for more details.

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

Cleaner BLAST Databases for More Accurate Results

LEGE — Tue, 23 Apr 2024 01:23:08 -0500

Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.

Foreign Contamination Screen tool for genome cross-species screening (FCS-GX) detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX)
Average Nucleotide Identity (ANI) evaluates the taxonomic classification of prokaryotic genome assemblies. Sequences from genomes marked up as ‘unverified source organism’ are considered suspect and removed.

Ref https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/