GC ( seq )

calculates G+C content

GC123 ( seq )

calculates totla G+C content plus first, second and third position

GC_Frame ( seq,  genetic_code=1 )

just an alias for six_frame_translations

GC_skew ( seq,  window=100 )

calculates GC skew (G-C)/(G+C)

antiparallel ( seq )

returns reversed complementary sequence ( = other strand )

apply_on_multi_fasta (
        file,
        function,
        *args,
        )

apply function on each sequence in a multiple FASTA file

complement ( seq )

returns the complementary sequence (NOT antiparallel)

fasta_uniqids ( file )

checks and changes the name/ID's to be unique identifiers by adding numbers

nt_search ( seq,  subseq )

search for a DNA subseq in sequence use ambiguous values (like N = A or T or C or G, R = A or G etc.) searches only on forward strand

quick_FASTA_reader ( file )

simple and FASTA reader, preferable to be used on large files

quicker_apply_on_multi_fasta (
        file,
        function,
        *args,
        )

apply function on each sequence in a multiple FASTA file

reverse ( seq )

reverse the sequence

seq3 ( seq )

Method that returns the amino acid sequence as a list of three letter codes. Output follows the IUPAC standard plus Ter for terminator. Any unknown character, including the default unknown character X, is changed into Xaa. A noncoded aminoacid selenocystein is recognized (Sel, U).

six_frame_translations ( seq,  genetic_code=1 )

nice looking 6 frame translation with GC content - code from xbbtools similar to DNA Striders six-frame translation

translate (
        seq,
        frame=1,
        genetic_code=1,
        translator=None,
        )

translation of DNA in one of the six different reading frames