[Bioperl-l] automation of translation based on alignment

[Florent Angly]

Hi Ross,

Please keep relies on the BioPerl mailing list so that everyone benefits.

You should give detailed explanations of what you are tying to achieve., 
e.g.:
     * What type of input file do you have?
     * Do you already know the location of the ORFs?
     * what is the multiple alignments you are talking about
...

Florent


On 22/03/10 11:07, Ross KK Leung wrote:
> Dear Florent,
>
> Thanks for your response. While the one with Genbank file can be extracted,
> those without have to rely on alignment. Scripts certainly can be written to
> move forward and backward on the multiple alignment but it is an error-prone
> process and that's why I raised this question.
>
> Rgds, Ross
>
>
>
> -----Original Message-----
> From: Florent Angly [mailto:florent.angly at gmail.com]
> Sent: Monday, March 22, 2010 8:44 AM
> To: Ross KK Leung
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] automation of translation based on alignment
>
> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>      
>
>
>