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. AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGA...2866 days ago
Extract a range from genome file with perl.
...rict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos =..._pos = $ARGV[2]; my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fast...a'); my $out = Bio::SeqIO->new( -file => ">$in_file.out", -format => 'fasta');...2641 days ago
Install ATOM editor on Elemantory OS / Ubuntu
#Download ATOM deb file from https://atom.io/ https://atom.io/download/...age gconf2-common. (Reading database ... 194272 files and directories currently in...2-common (3.2.6-4ubuntu1) ... Creating config file /etc/gconf/2/path with new ve...1190 days ago
2718 days ago
2707 days ago
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->new(-file => ">$file.uniq", -format =>...2704 days ago
Perl script to insert the DNA string in genome
...se warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARG...insertion my $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file); my $seq_out = Bio...2673 days ago
Calculate ATGC percentage in parallel with perl
...n/perl use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fa...2670 days ago
Calculate some statistics for a DNA alignment with Perl
...io::AlignIO->new(-format => 'emboss', -file => 't/data/insulin.water');...in = Bio::AlignIO->new(-format => 'fasta', -file => 't/data/nei_gojobori_tes...2663 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2631 days ago