Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the...', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin',...cs::R', 'Math::Round', 'File::Find', 'Bio::...1152 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file...asta"; # read genome sequence my $seqio = Bio::SeqIO->new(-file => $genome_...eqobj->seq(); # run RepeatMasker my $rm = Bio::...422 days ago
91 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gff'; my $genome_fa...91 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format.../to/your/input.fasta'; # Step 1: Read the input FASTA file my $seqio = Bio::...91 days ago
Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate()...91 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta'; # Create Bio::...91 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variables for comput...91 days ago