Subject: Re: [Bug 2381] back-translate - msg#00083

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[Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0

http://bugzilla.open-bio.org/show_bug.cgi?id=2361 ------- Comment #37 from biopython-bugzilla@xxxxxxxxxxxxxxxxxxxxx 2007-10-19 08:38 EST ------- I would have suggested adding a mxTextTools version check to test_GenBankFormat.py and throwing the external dependancy error is 3.0 is found. That would "solve" the problem test case, and after the next release we could begin the process of deprecating the modules you suggested. But I'm OK with your suggestion Michiel (comment 36), although it seems a little drastic. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.

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Re: [Bug 2381] back-translate

Yes, I know it's a one-to-many mapping. But that's why it's nice to have a handy subroutine for doing it. For codon optimization, all possible back translations with unambiguous nucleotides would be best. Then, one evaluates some objective function over all possible sequences to find an optimal one. Optimality depends on the application, but eliminating restriction sites, avoiding certain repetitive or transposon sequences, etc is very common. For searching for homologous proteins, it would be best to have the back-translate function produce something that could be fed into an alignment program or regexp expression. Then, one could align a database of sequences with your back-translated protein to determine which sequence is most similar to your protein. Basically, this is what BlastP does (you might want to look up its algorithm to determine a good way of doing this, if you wish to reproduce it in Biopython or, otherwise, rely on the NCBI webserver). What does the current back-translate function output? -Howard On 10/19/07, Peter <biopython-dev@xxxxxxxxxxxxxxxxxxxxx> wrote: > Howard Salis wrote: > > Yes. Back-translating a sequence is important in codon optimization, > > searching for homologous proteins, etc. > > Unlike forward translation, transcription, back-transcription, > complements and reverse complements, back-translation is not a > one-to-one mapping. > > In your examples, would you want to know all: > - all possible back translations (as unambigous nucleotides) > - all possible back translations (as ambigous nucleotides) > - a possible back translation (using ambiguous nucleotides) > - a possible back translation (using un-ambiguous nucleotides) > > For example, back translating an Tyr => UAC or UAU => UAW (nice and > clear - we can represent this perfectly with a single ambiguous codon). > On the other hand, Arg => AGA, AGG, CGA, CGC, CGG, CGU => AGR or CGN > > Oh, and would you expect DNA or RNA back? > > Peter > >

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Re: [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)

Yes. Back-translating a sequence is important in codon optimization, searching for homologous proteins, etc. > > - back_translate (gives a single possible nucleotide sequence) > Does anybody actually use this function? > > > -- > Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@xxxxxxxxxxxxxxxxxx > http://lists.open-bio.org/mailman/listinfo/biopython-dev >

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Re: [Bug 2381] back-translate

Yes, I know it's a one-to-many mapping. But that's why it's nice to have a handy subroutine for doing it. For codon optimization, all possible back translations with unambiguous nucleotides would be best. Then, one evaluates some objective function over all possible sequences to find an optimal one. Optimality depends on the application, but eliminating restriction sites, avoiding certain repetitive or transposon sequences, etc is very common. For searching for homologous proteins, it would be best to have the back-translate function produce something that could be fed into an alignment program or regexp expression. Then, one could align a database of sequences with your back-translated protein to determine which sequence is most similar to your protein. Basically, this is what BlastP does (you might want to look up its algorithm to determine a good way of doing this, if you wish to reproduce it in Biopython or, otherwise, rely on the NCBI webserver). What does the current back-translate function output? -Howard On 10/19/07, Peter <biopython-dev@xxxxxxxxxxxxxxxxxxxxx> wrote: > Howard Salis wrote: > > Yes. Back-translating a sequence is important in codon optimization, > > searching for homologous proteins, etc. > > Unlike forward translation, transcription, back-transcription, > complements and reverse complements, back-translation is not a > one-to-one mapping. > > In your examples, would you want to know all: > - all possible back translations (as unambigous nucleotides) > - all possible back translations (as ambigous nucleotides) > - a possible back translation (using ambiguous nucleotides) > - a possible back translation (using un-ambiguous nucleotides) > > For example, back translating an Tyr => UAC or UAU => UAW (nice and > clear - we can represent this perfectly with a single ambiguous codon). > On the other hand, Arg => AGA, AGG, CGA, CGC, CGG, CGU => AGR or CGN > > Oh, and would you expect DNA or RNA back? > > Peter > >