92 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 $gen...92 days ago
Perl script for six frame translation !
...ict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my...ead the input FASTA file my $seqio = Bio::SeqIO->new(-file =>...frames) { my $translated_seq = translate_frame($sequence,...>translate(-frame => $frame)->seq; } else { # If...92 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(...late() return translated_seq def six_frame_translation(...quence = translate_frame(record.seq, frame) frame_ty...92 days ago
Perl script to calculate the basic stats of the assembled genome !
.../bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing...ile = 'genome_assembly.fasta'; # Create Bio::SeqIO object to read the FASTA fi...my @contig_lengths; # Iterate through each sequence in the assembly while (...92 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembl...0 num_contigs = 0 contig_lengths = [] # Iterate through each sequence in the assembly for record in SeqIO.parse(input_file, 'fasta'):...92 days ago
46 days ago