BOL

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

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/

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

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

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

#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

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

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

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

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

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

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

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

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

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