[Arthropod] Re: EST assembly correction

[Yannick Wurm]

Thanks for the reply Mark, I'll look into that.
best,
yannick

On 8 Dec 2009, at 18:03, arthropod-request from oat.bio.indiana.edu wrote:
> Hi
> 
> Using a 'good' est translator such as prot4est will autocorrect for  
> these errors, and will also autocorrect errors in 'novel' genes that  
> have codon usage biases that can be recognised.
> Prot4EST is about to be released in a new all signing version... see http://www.nematodes.org/bioinformatics/prot4EST/index.shtml 
>  for version 2; but version 3 is better.
> Mark
> 
> On 7 Dec 2009, at 06:25, Yannick Wurm wrote:
> 
>> Hello all,
>> 
>> thanks Don for setting up this list.
>> 
>> I'm just finishing my PhD in Lausanne, Switzerland, working with  
>> some EST data from ants (the closest high quality genomes are the  
>> Nasonia wasp and the Honeybee).
>> 
>> One issue with 454 data are homopolymer errors (AAAAAAA may become  
>> AAAAAA or AAAAAAAA according to the 454 basecaller). When in a  
>> coding sequence, something like that leads to frameshifts and thus  
>> bad protein models. It should be possible to correct for this kind  
>> of error (and insertions/deletions in EST data in general) by using  
>> alignments obtained from blastx against a database of good proteins.
>> 
>> Have any list members done this?
>> 
>> Kind regards,
>> 
>> Yannick
>> 
>>