Abhimanyu Singh
A bioinformatics beginner
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SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2172 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2295 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...NCBI PSI-BLAST Tutorial
By Jitendra Narayan 4110 days agohttp:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are...A fast package to parse BLAST
By Jitendra Narayan 4091 days ago, managBlaSTorage: a fast package to parsee and store BLAST resultsBLAST Ring Image Generator (BRIG)
By Anjana 2975 days agobrig.sourceforge.net - BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:...
Converting BLAST output into CSV
Last updated 2539 days ago by Poonam MahapatraSuppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific...BLAST+ 2.11.0 release is now available on FTP site !
By Jit 1469 days agoThe main advance is the ability to provide usage reports to NCBI to help us improve BLAST.-
Understanding BLASTn output format 6 !
Last updated 2340 days ago by Rahul NayakBLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident... BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2357 days agowww.animalgenome.org - 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...
