[Biopython-dev] [Bug 2618] back_translate method for the Seq object (in Bio.Seq)?

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http://bugzilla.open-bio.org/show_bug.cgi?id=2618





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-16 12:09 EST -------
Created an attachment (id=1009)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1009&action=view)
Patch to Bio/Seq.py for back translation

This follows Bio.Translate and simply uses whatever arbitrary unambiguous codon
Bio.Data.CodonTable object supplies via its back_table.

e.g.

>>> from Bio import Seq
>>> Seq("ACBDEF*").back_translate()
Seq('GCUUGUNNNGAUGAGUUUUAA', IUPACAmbiguousRNA())
>>> Seq("ACBDEF*").back_translate().translate()
Seq('ACXDEF*', HasStopCodon(ExtendedIUPACProtein(), '*'))

If instead we want to return ambiguous codons (e.g. "P" -> "CCN"), then
handling of back-transcription of special cases B (R/N) and J (I/L) or Z (E/Q)
could also be improved (here just "NNN" is used).

e.g. For the standard table, "SAR" codes for "Z".  I haven't checked if
something this is possible for all B, J and Z for all NCBI codon tables.


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