[Arthropod] EST assembly correction

Mark Blaxter via arthropod%40net.bio.net (by mark.blaxter from ed.ac.uk)
Mon Dec 7 11:07:03 EST 2009


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
>
>
>
>
> --------------------------------------------
>          yannick . wurm @ unil . ch
> Ant Genomics, Ecology & Evolution @ Lausanne
>   http://www.unil.ch/dee/page28685_fr.html
>
>
>
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Mark Blaxter
mark.blaxter from ed.ac.uk

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