Prediction the function of Novel gene(s)!

R. Jayakumar jakku at mrna.tn.nic.in
Thu Jun 14 09:42:20 EST 2001


hi..
   partial sequences will do fine, to find what kind of gene they are.  what
you should do is this - First of all make sure there is no sequencing errors
there.  The check out the ORFs in all possible frames (6 possibilities)  If
the sequence is an internal part of a gene, then you should get an open ORF
with no start or end.  But take care to see whether there are any sequencing
errors like insertion or deletion of a bp which can cause a frameshift.
Take the open frame, translate the protein for that frame and use a normal
blastp or a blastx (if you want to use the DNA sequence) and that should
pick out the gene from the database.  Sometimes, i submit the sequence as
such and do a FASTA (at www.ebi.ac.uk) with it for identifying the sequence.
But this is not adivsable because of codon degeneracy and ATGC bias problem.
So it is always advisable to translate it into a protein sequence and then
to do the BLASTing.
    I normally use the FRAMES tool in GCG for the ORF checking.  But there
are other softwares at www.ebi.ac.uk website called GENEMARK (but not very
satisfactory) for doing this.  You can also search for ESTs within your
sequences to check out whether they are significant.   You can also do a
motif search in the protein sequence.. you should try PREDICTPROTEIN or
PROTPARAM with the translated protein.. that should help a lot.
   best of luck
jayakumar

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R. Jayakumar
Dept. of Molecular Microbiology,
School of Biotechnology,
Madurai Kamaraj University,
Madurai - 625021. India.
tel: +91-452-859141(night hours), +91-452-858471 (ask to connect to 374)
fax:+91-452-859105
Efax: (603)-688-4665
Email: jakkku at mrna.tn.nic.in, (send a copy to jakku at zxmail.com ....just in
case)
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Science is constructed of facts like a house is of bricks, but a mere
accumulation of facts does not make science nor does a pile of bricks a
house
-Henri Poincare
----- Original Message -----
From: "Terry Lau" <lauck at hkucc.hku.hk>
To: <methods at hgmp.mrc.ac.uk>
Sent: Thursday, June 14, 2001 2:52 PM
Subject: Prediction the function of Novel gene(s)!


> Dear All,
>
> Would it have some websites that can be used to find out the function or
> functional domains of some novel genes? [But I only have the partial
> sequence of such gene(s)] I have used the sofeware from NCBI website and
> I want to search other websites.
>
> Thanks in advance!
>
>
>
> Terry!
>
>

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