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...151 days ago
Raku script to find repeats in sequences !
sub find-repeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($sequence.chars - $min-repeat-length + 1) -> $i { my $substring = $sequence.sub...151 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+min_re...151 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length = 2, $max-repeat-length = 6, $min-repeat-count = 3) { my @microsatellites; for my $repeat-length ($min-rep...151 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'; # C...151 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 computing st...151 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq: with open(fasta_file, 'w') as fa: while True: # Rea...95 days ago
Python script to finds extact similar sequence between two multi fasta files !
from Bio.Blast.Applications import NcbiblastnCommandline import os import sys def perform_local_blast(query_file, subject_file, output_file): # Set up the BLAST co...60 days ago
Python script to create fastq file with random sequences
import random def generate_random_sequence(length): bases = ['A', 'C', 'G', 'T'] return ''.join(random.choice(bases) for _ in range(length)) def generate_ran...20 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variables to store genome statistics genome_length = 0 gc_count = 0 a_count...20 days ago