[Bioperl-l] New to bioperl

Bradyjoel joel.klein at wur.nl
Tue Jan 24 09:46:05 EST 2012


Hi Roy,

Thank you for your quick reply, I already tried xbase and it finds some of
the exopolysacharide biosynthesis genes that I’m looking for but only the
genes that are already annotated in the other organisms. I also tried to
merge these results but it still misses some of the genes  or the correct
annotation and merging also cost a lot of time. Since I am only looking for
a certain set of genes, I thought it might be easier to use a certain script
that can blast these these protein queries and add the annotation at the
locations were it finds simularity in my sequence. I already tried to make a
script myself but I'm still troubled how to connect the output of ablast to
the action of adding the gene information and write it to a certain file. 

Joel


Roy Chaudhuri-3 wrote:
> 
> Hi Joel,
> 
> This is possible using BioPerl, but it may be simpler to use an online 
> automated annotation service eg:
> http://www.xbase.ac.uk/annotation
> 
> Roy.
> 
> On 24/01/2012 13:38, Bradyjoel wrote:
>>
>> Hi all,
>>
>> I'm somewhat new to the bioinformatics but I need to annotate a newly
>> sequenced bacterial genome based on some known proteins amino acid
>> sequences
>> from a neighbouring organism. I've been doing this manually with tblastn
>> and
>> then search and annotated this in artemis. However I have an entire
>> directory full of these protein sequences and was wondering if this could
>> be
>> automated in such way that I have an input nucleotide sequence consisting
>> of
>> contigs which are automatically translated in frames and then aligned and
>> annotated with the known protein amino acid sequences. If you could help
>> me
>> with writing such a script I would be very grateful.
>>
>> Joel
>>
>>
>>
> 
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> 
> 

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