[BiO BB] EST mapping

[Dan Bolser]

2009/9/16 Kie Kyon Huang <kiekyon.huang at gmail.com>:
> Hi all,
>
> I need to map my EST data to a fungal genome.  The goal here is to
> evaluate the accuracy of the gene prediction data.
>
> At the moment, all I have is fasta file containing the entire genome,
> the ESTs, and the predicted genes respectively.
>
> Can anyone point me to the correct tools/softwares to achieve this?

First you need a tool to align the ESTs to the genome. Many tools will
do this. I'd suggest Blast or MUMmer, but their are others.

Next you need software to compare your gene predictions to the
alignments to check that they coincide (and to measure the degree of
coincidence). Off hand I don't know of any specific tool to do this
(although I'd be surprised if there wasn't something that you could
use).

However, given the specifics of the problem, you may be best off just
processing the data yourself, and measuring your own 'coincidence
statistic'. To do this you could use something like BioPerl, BioPython
or BioJava, etc. These libraries will make processing the data a
little easier, but at the expense of learning the overall library
design.

HTH,
Dan.



> Thanks a lot.
>
> Huang
>
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