BOL: Related items

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+ 2.11.0 release is now available on FTP site !

Jit — Sat, 14 Nov 2020 21:37:53 -0600

BLAST+ 2.11.0 release is now available from our FTP site. The main advance is the ability to provide usage reports to NCBI to help us improve BLAST. This information is limited to the name of the BLAST program, some basic database metadata, a few BLAST parameters, as well the number and total size of your queries. See the Privacy document for more details on the information we collect, how we will use it, and how you can opt-out of reporting.

Another new feature allows threading by query batch in rpsblast/rpstblastn. Enabling this option using -m t provides more efficient searching with large numbers of queries. See release notes for details on more improvements and bug fixes.

Useful Links
------------
NCBI Insights: https://ncbiinsights.ncbi.nlm.nih.gov/2020/11/12/blast-2-11-0/

BLAST FTP: https://go.usa.gov/x7QQ3
Privacy document: https://go.usa.gov/x7QQe
Release notes: https://go.usa.gov/x7Qnv

Basics of BLAST Programs !

BioStar — Fri, 26 Jul 2024 06:04:26 -0500

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

REST API

Neel — Mon, 04 Oct 2021 12:46:40 -0500

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.

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

Convert VCF to tab-deilimited table

Seema Singh — Tue, 15 May 2018 07:39:08 -0500

Performed with GATK :

java -Xmx8g -jar GenomeAnalysisTK.jar \
-T VariantsToTable \
-R reference.fa \
-V reference_genomes_GT.vcf \
-F CHROM -F POS -F REF -F ALT -GF GT \
-o reference_genomes_GT.table
multiple_sample.vcf should also be converted to multiple_sample_GT.table using this approach.

vcf2maf convert !

Surabhi Chaudhary — Fri, 17 Dec 2021 03:20:01 -0600

To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a Missense_Mutation close enough to a Splice_Site, can be labeled as either in MAF format, but not as both. This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize. The vcf2maf and maf2maf scripts leave most of that responsibility to Ensembl's VEP, but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the extensive support in parsing a wide range of crappy MAF-like or VCF-like formats we've seen out in the wild.

Address of the bookmark: https://github.com/mskcc/vcf2maf

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Thu, 14 May 2020 15:13:30 -0500

gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/

Address of the bookmark: https://github.com/kammoji/gapFinisher

BOL: Related items

Genome Workbench 2.10.7

DIAMOND

BLAST+ 2.11.0 release is now available on FTP site !

Basics of BLAST Programs !

REST API

REST API

Python

BEAP: Blast Extension and Assembly Program

Convert VCF to tab-deilimited table

vcf2maf convert !

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output