[Bioperl-l] automation of translation based on alignment

[Florent Angly]

Hi Ross,
It seems like your answer is in the link you put. On this link, all the 
coding sequences are already identified and their aminoacid sequence 
provided. You simply need to parse all the GenBank entries to extract 
this information. You may use EUtilities to achieve this online: 
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
Florent

On 21/03/10 09:55, Ross KK Leung wrote:
> Dear bioperl users,
>
>
>
> I am working on virus sequences and one of the Genbank file is here:
>
>
>
> http://www.ncbi.nlm.nih.gov/nuccore/DQ089804.1?ordinalpos=1
> <http://www.ncbi.nlm.nih.gov/nuccore/DQ089804.1?ordinalpos=1&itool=EntrezSys
> tem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum>
> &itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSu
> m
>
>
>
> with 1000 such nucleotide sequences, I'd like to translate the corresponding
> protein coding sequences. The difficulties lie in:
>
>
>
> 1)      The genome sequence is circular
>
> 2)      The genes are overlapping
>
>
>
> I don't have all the 1000 Genbank files but I plan to use the above guide
> one to direct the automation process. Has bioperl implemented specialized
> functions to handle this kind of problem?
>
>
>
> Thanks a lot for your advice, Ross
>
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