2916 days ago
2916 days ago
Perl script to insert sequence in contig !!
...nsertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CONTIG , $LOC , -length($CONTIG) ) = $SEQ ; return...2752 days ago
2748 days ago
2737 days ago
Perl script to insert the DNA string in genome
...IO->new( -format => 'fasta',-file => ">".$out); while( my $seq = $seq_in->next_seq() ) { if($seq->primary_id eq $chr){ my $length = length($seq->seq); my $...2703 days ago
Calculate ATGC percentage in parallel with perl
...$pm->wait_all_children; print "Everybody is out of the pool!\n"; sub checkATCG { my $name=shift; my $DNA=$sequences{$name}; my $length=length $DNA; my $a=($DNA=~tr/A//);...2700 days ago
BASH script for SelfBLAST a genome
...egablast -query $SEQ -db $MYDB -evalue 1e-5 -num_threads $THREAD -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sseqid sstart send evalue length frames qcovs' -out $OUTFILE;...2696 days ago
Extract fasta sequence from a multifasta file with coordinates
...y $seqstr = $db->seq('CHROMOSOME_I', 4_000_000 => 4_100_000); my $revseq = $db->seq('CHROMOSOME_I', 4_100_000 => 4_000_000); my $length = $db->length('CHROMOSOME_I'); my $heade...2576 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2382 days ago