[BioPython] Re: translating genes with >1 exon

[Cayte]

----- Original Message ----- 
From: Andrew Dalke <dalke@acm.org>
To: <biopython@biopython.org>
Sent: Monday, April 10, 2000 9:41 AM
Subject: [BioPython] Re: translating genes with >1 exon


> On the bioperl list, Keith James asked about translating
> an exon:
> > Get the PrimarySeq object of each subsequence
> > Get the sequence string of each PrimarySeq object
> > Join the sequence strings together
> > Make a new PrimarySeq object from the string
> > Translate that, making yet another PrimarySeq object
> 
> In the proposal code I've been working on, I added
> __add__ (and I should add __radd__), so you can do
> 
> s1 = Seq("ATGCATCACAATCG", Alphabet.IUPAC.unambiguous_dna)
> s2 = Seq("W", Alphabet.IUPAC.ambiguous_dna)
> t = s1 + s2
> 
> and get that t is
> 
> Seq("ATGCATCACAATCGW", IUPACAmbiguousDNA())
> 
> Thus, translation of subsets is:
>   translate(seq[5:20] + seq[29:65] + seq[100:200])
> 
   Should there be a program to guess where the exon start and end?

                                              Cayte