BOL: Wire posts tagged with 'Sequence'

Wire post by Jit

Jit — Thu, 22 Aug 2019 12:39:32 -0500

Alignment-free sequence comparison: benefits, applications, and tools https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1319-7 #Alignment #Sequence

Wire post by BioStar

BioStar — Fri, 01 Feb 2019 09:01:02 -0600

The aim of this program suite is to support checks of #Sequence #Variant #Nomenclature according to the guidelines of the #Human #Genome #Variation Society. https://www.mutalyzer.nl/

Wire post by Jit

Jit — Thu, 10 Jan 2019 19:11:53 -0600

Recommendations for the description of #sequence #variants https://www.hgvs.org/mutnomen/recs.html

Wire post by Manisha Mishra

Manisha Mishra — Tue, 17 Apr 2018 16:37:42 -0500

Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

Wire post by Rahul Nayak

Rahul Nayak — Wed, 14 Mar 2018 10:31:04 -0500

Get the sequences using coordinates in bed file. $ bedtools getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #bedtools

Wire post by Jit

Jit — Thu, 14 Dec 2017 04:55:21 -0600

#Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

Wire post by Abhimanyu Singh

Abhimanyu Singh — Mon, 13 Mar 2017 08:28:36 -0500

#Random #sequence generator with #perloneliner : $ perl -e '$x=int(rand(1000)); printf( "chr1\t%s\t%s", $x, $x + 10)'

Wire post by Abhimanyu Singh

Abhimanyu Singh — Mon, 13 Mar 2017 06:13:21 -0500

#Extract a #sequence from #multi-fasta file: $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file

Wire post by Jit

Jit — Fri, 24 Feb 2017 04:49:20 -0600

AVID: A Global Alignment Program https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/ #AVID #Alignment #Global #Sequence #Genome

Wire post by Neel

Neel — Wed, 06 Apr 2016 05:23:03 -0500

PAired-eND Assembler for DNA sequences https://github.com/neufeld/pandaseq #Sequence #Assembler #PANDAseq

Wire post by Archana Malhotra

Archana Malhotra — Fri, 01 Apr 2016 11:14:43 -0500

Dynamic programming http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html #Programming #Alignment #Sequence #Dynamic

Wire post by Neel

Neel — Tue, 22 Mar 2016 04:35:32 -0500

A powerful #multiple #sequence #alignment #browser http://wasabiapp.org/

Wire post by Rahul Nayak

Rahul Nayak — Mon, 28 Sep 2015 10:16:16 -0500

The BLAST parser http://kirill-kryukov.com/study/tools/blast-parser/ #BLAST #Parser #Genome #Match #Sequence #Similarity

Wire post by Jitendra Narayan

Jitendra Narayan — Mon, 24 Nov 2014 16:33:14 -0600

Seqloc: Handle sequence locations for bioinformatics https://hackage.haskell.org/package/seqloc-0.6 #Sequence #Location #Package

Wire post by Rahul Nayak

Rahul Nayak — Fri, 14 Nov 2014 16:44:46 -0600

Sequence analysis http://bio.lundberg.gu.se/courses/ht03/bio1/bio1_e2b.html #Sequence #Alignment #Algorithms #C #C++