2866 days ago
2866 days ago
2866 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 gen...$ makeblastdb -dbtype nucl -out EC -in EC4115.fa -parse_seqids # retre...head >lcl|NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome,...2846 days ago
2687 days ago
2687 days ago
Perl script to remove the duplicate sequences from multifasta file
...) { my $id = $seqs->display_id; my $seq = $seqs->seq; unless(exists($unique{$seq})) { $outseq->write_seq($seqs); $unique{$seq} +=1; } }2684 days ago
Perl script to insert the DNA string in genome
...my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fasta file my $chr="test"; #insertion chromosome my $pos=10; # position of the insertion...2653 days ago
Calculate ATGC percentage in parallel with perl
...my $c=($DNA=~tr/G//); my $d=($DNA=~tr/T//); my $Total=$a+$b+$c+$d; my $GC=($DNA=~s/GC/GC/g); my $AT=($DNA=~s/AT/AT/g); my $GCper=($GC/($Total)*100); print"$name\t$Total\t$AT...2650 days ago
BASH script for SelfBLAST a genome
...blastdb -in $FASTAFILE -parse_seqids -dbtype nucl -out $MYDB fi if [ $1 = "extract" ] then echo "...ta samtools faidx MergedContigs.fasta $2 > $2.fa SEQ=$2.fa elif [ $1 = "all" ] then echo "You...2646 days ago