[BiO BB] Starting point EST annotation/grouping

Ahmed Moustafa ahmed at pobox.com
Fri Aug 11 17:00:15 EDT 2006


Hi Alex,

Thank you so much for your reply.

How do you generate the unigene list after assembling the ESTs?

Thanks again!

Ahmed

On 8/11/06, Bossers, Alex <Alex.Bossers at wur.nl> wrote:
>
>  Ahmed,
>
>
>
> No I did not use the PHRED/PHRAP/CONSED package for this (I did try it but
> found the TGICL suite more appropriate for ESTs).
>
> http://www.tigr.org/tdb/tgi/software/
>
> For basecalling I used a windows platform based caller since PHRED at that
> time did not support our used dyes for sequencing.. :(
>
> Thereafter the TGICL basically uses megablast to cluster all sequences
> into groups and than assembles it using the cap3 assembler.
>
>
>
> Clustering and assembling is always difficult to explain. As far as I
> understand the clustering of large groups of sequences speeds up the second
> step; assembling. Basically you end up with contigs (having more than one
> sequence) or singletons.
>
>
>
> With unigene list I mean a list of all different genes present in my
> sample of 13k. Like the Gene indices lists of species present at TIGR.
> http://www.tigr.org/tdb/tgi/index.shtml
>
>
>
>
>
> Now the next steps.
>
>
>
> Alex
>
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