[Computational-biology] 454 ESTs Assembly

[Amit Dattatreya Parhar]

Hi,

We are going to perform an EST assembly project based on 454 data. And
although 454 has a software for assembly (I feel that it is not good enough
for repetitive or Eukaryotic genomes) . Would CAP3 or PCAP do decent job if
I feed the program with assembled contigs from 454 software say length
approx. 200 bps?
will this two stage strategy would work?

Is there any other open source software available which do the job
efficiently?

Thanks in advance.

regards,
Amit


----- Original Message ----- 
From: <comp-bio-request from oat.bio.indiana.edu>
To: <comp-bio from magpie.bio.indiana.edu>
Sent: Tuesday, August 07, 2007 10:30 PM
Subject: Comp-bio Digest, Vol 27, Issue 5


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> Today's Topics:
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>    1. How to use FoldX (???)
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> Message: 1
> Date: Tue, 7 Aug 2007 01:57:35 +0900
> From: ??? <ambition from postech.ac.kr>
> Subject: [Computational-biology] How to use FoldX
> To: <comp-bio from magpie.bio.indiana.edu>
> Message-ID: <000f01c7d84a$e325bff0$4f82df8d from user1gggdafd>
> Content-Type: text/plain; charset="ks_c_5601-1987"
>
> Hello,
>
>
>
> I¡¯d like to use the FoldX at linux server in my lab in order to predict
> the mutation effects of certain protein structure.
>
> But I found it is quite difficult to run it because I couldn¡¯t figure out
> how to make runfile.
>
>
>
> Is there anybody who can show me a simple example of runfile to predict
the
> mutation effect?
>
> If I want to change alanine residue (residue number 3) of chain B in
> 1XXX.pdb to valine with all the other options as default, what the runfile
> will be?
>
>
>
>
>
> And if you know the better mutation effect prediction tool (based on the
> PDB structure as input), please let me know.
>
> Thank you.
>
>
>
>
>
>
>
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