pybbiology

Freely available tools for Analsis of DNA
The Biopython Project is an international association of developers
of freely available Python tools for computational molecular biology.

List of functions and usage

• seq_percent(dna_sequence,*char)
• has_stop_codon(dna,frame=0)

1. compute DNA sequence

def seq_percent(dna_sequence,*char):
        sum=0
        listed=[]
        dna_length=len(dna_sequence)
        for arg in char:
            if listed.count(arg)==0:
                sum= sum + dna_sequence.count(arg)
                listed.append(arg)
        return (sum)*100.0/dna_length

2. This function checks if given DNA has in frame stop codons.

def has_stop_codon(dna,frame=0):
    stop_codon_found=False
    stop_codons=['tga','tag','taa']
    for i in range(frame,len(dna),3):
        codon=dna[i:i+3].lower()
        if codon in stop_codons:
            stop_codon_found=True
            break
    return stop_codon_found