[Bioperl-l] automation of translation based on alignment

[Ross KK Leung]

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