Perl script to find inverted repeats !
...in/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker;...sta"; # read genome sequence my $seqio = Bio::SeqIO->new(-file => $genome_...qobj->seq(); # run RepeatMasker my $rm = Bio::Tools::Run::RepeatMasker->ne...419 days ago
88 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_fasta =...88 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence f...o/your/input.fasta'; # Step 1: Read the input FASTA file my $seqio = Bio::SeqIO->new(-file => $input_f...88 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() else:...88 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 assembl...y in FASTA format my $input_file = 'genome_assembly.fasta'; # Create Bio::SeqIO object to read the FAS...88 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 computin...88 days ago