Perl script to insert the DNA string in genome
...warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # in...# position of the insertion my $seqI = "AAAA"; #sequence of the i...,-file => ">".$out); while( my $seq = $seq_in->next_seq() ) {...bj); } else{ $seq_out->write_seq($seq); }...2651 days ago
Calculate ATGC percentage in parallel with perl
...allel::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqI...format => "fasta"); while(my$seqobj = $seqio->next_seq) {...ocs = 5; my @names = keys %sequences; # hash to resolve...{ my $name=shift; my $DNA=$sequences{$name}; my $length=len...2648 days ago
BASH script for SelfBLAST a genome
...gs.fasta MYDB=myDB OUTFILE=seeRES THREAD=20 SEQ="" echo "User $USER provid...for you"; makeblastdb -in $FASTAFILE -parse_seqids -dbtype nucl -out $MYDB f...f [ $1 = "all" ] then echo "You want entire sequence to blast" SEQ=$FASTAF...2644 days ago
Calculate some statistics for a DNA alignment with Perl
...t/data/nei_gojobori_test.aln'); my $alnobj = $in->next_aln; my ($seq1id,$seq2id) = map { $_->display_id }...ge_KaKs($alnobj, 1000); for (sort keys %$result3 ){ next if /Seq/; printf("%-9s %.4f \n...2642 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; u...my ($header) = "$/$1_$start-$end\n"; my $seq = ${^POSTMATCH}; $seq =~...s//g; print $header; print +( substr $seq, $start - 1, $end ) . "\n";...2614 days ago
Palindrome Simulation commands !
...~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/seqtk mergepe paired_dat1.fq pair...1728 days ago
Extract fasta sequence from a multifasta file with coordinates
...ary_ids; foreach my $id (@ids) { my $sequence = $db->seq($id, $querySizeST => $querySi...all_primary_ids; # Simple access my $seqstr = $db->seq('CHROMOSOME_I...eq_stream; while (my $seq = $stream->next_seq) { # Bio::PrimarySeqI st...2525 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2331 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2461 days ago
Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2363 days ago