vbio

reverse_complement(dna)

Gives back the reverse complement of a DNA sequence.

reverse_complement("ATGC")

transcribe(dna)

Transcribes a DNA sequence into RNA by swapping every T for a U.

transcribe("ATGC")

translate(rna)

Translates an RNA sequence into a protein, stopping at the first in-frame stop codon.

translate("AUGGCCUAA")

gc_content(sequence)

gc_content("ATGC")

hamming_distance(a, b)

Counts the positions at which two of equal length sequences differ.

hamming_distance("GAGCCTACTAACGGGAT", "CATCGTAATGACGGCCT")

find_orfs(dna)

Finds every open reading frame on the forward strand of a DNA sequence.

find_orfs("ATGAAATAG")

parse_fasta(text)

Parses FASTA-formatted text into a list of (header, sequence) records.

parse_fasta(">seq1\nACGT\n>seq2\nTTAA")

codon_usage(dna)

Counts how many times each codon appears in a DNA sequence.

codon_usage("ATGATG")

melting_temperature(primer)

Estimates a short primer's melting temperature using the Wallace rule.

melting_temperature("ACGTACGTAA")