[Arthropod] Re: EST assembly correction
(by yannick.wurm from unil.ch)
Wed Dec 9 12:43:52 EST 2009
Thanks for the reply Mark, I'll look into that.
On 8 Dec 2009, at 18:03, arthropod-request from oat.bio.indiana.edu wrote:
> 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.
> 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,
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