Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extractSeq...2928 days ago
2924 days ago
Perl script introduces control structures, arrays and hashes.
#!/usr/bin/env perl use strict; use warnings; my @first_array = ('DNA', 'ATGCGTGC', 5,...'Number of seqs' => 2 ); print $sequence{...Control Loop: foreach foreach my $key (sort (keys %sequence))...2915 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAA...2905 days ago
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CONTIG , $LOC , -len...2761 days ago
2757 days ago
2746 days ago
Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $A...#insertion chromosome my $pos=10; # position of the insertion my $seqI = "AAAA"; #sequence o...2712 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtoo...ct" ] then echo "Extracting the sequence $2 for you from $FASTAFILE --...l" ] then echo "You want entire sequence to blast" SEQ=$FASTAFILE e...ontact jitendra" fi echo "Doing alignments...2705 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...2702 days ago