[BiO BB] how to find conserved genes among viral genomes?

[Mahmoud ElHefnawi]

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" <marchywka at hotmail.com>
To: <bbb at bioinformatics.org>
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: bbb at bioinformatics.org
> 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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>>
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