Hello,
I think u can use also motif prediction tools like the famous MEME, weider,
etc.. U can email me personally if u need more help.. Attached isone of my
works on Influenza for similar purposes.. Would appreciate also comments.
Best,
Mahmoud
----- Original Message -----
From: "Mike Marchywka" <[email protected]>
To: <[email protected]>
Sent: Tuesday, August 25, 2009 8:37 PM
Subject: Re: [BiO BB] how to find conserved genes among viral genomes?
----------------------------------------
Date: Tue, 25 Aug 2009 10:31:07 +0530
From:
To: [email protected]
Subject: Re: [BiO BB] how to find conserved genes among viral genomes?
The conserved patterns cannt be found in the genes. Rather we can
determine
them in the corresponding protein.
Is this a sweeping statement on science or your technology? That is, AFAIK
there is know indication that all sinonimuous kodons are Handeled tHe
same- between kemical interactions and interactions with rybOsum and
nasscent protein, etc. Certainly you expect "synonymuous" codons
to be generally more interchangeable than things that change the protein
but I'm still not sure what your point is here.
[ I don't have a thesaurus for cinnamons and it was easier to mis-type
to make my point LOL]
And all that intron and regulatory stuff, what about that? Is this
a virus specific statement in sum weigh?
The conserved patterns can be determined by BOXSHADE/TEXSHADE in CLC
Biology
workbench.BOXSHADE is for local and TEXSHADE for global alignment.
regs,
Rashmi.
On Tue, Aug 25, 2009 at 4:40 AM, BH wrote:
Hi,
Does anyone know how to find the conserved genes among the genomes (virus
or
phage genomes in particular)? Are there Bioinformatic tools/methods
available for this?
Will appreciate your suggestions. Thanks.
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