[BiO BB] doubt in protein modeling step

[nikhil gadewal]

Hi kiran,

Both your doubt can be solved. But it is better to go
with first one. You can build consensus sequence by
multiple alignment taking into consideration of query
sequence also by using Bio-edit program which is
freeware.

regards,
NIKHIL 

--- Ayyagari Kiran <kiran_ayyagari at yahoo.com> wrote:
> Hi all,
> In protein modeling,at first we look for protein
> sequence similarity and doing Multiple Seq
> alignment. 
> Supposing I take 5 protein sequences hits (after
> doing
> Blastp),assuming that there are no pdb structures
> for
> any of them but still i have to model my protein
> sequence. 
> the next step is to go for Multiple sequence
> alignment
> where in we can find out which are the regions
> exactly
> conserved and find whether those regions have any
> structural similarity also!!!
> 
> But here the input for Multiple Sequence alignment
> is
> our query sequence + the 5 similar 
> sequences having highest hits (from BLAST)
> 
> my question is whether we can/should build a
> consensus
> sequence by multiple alignment taking into
> consideration our query sequence also??
> 
> or build a consensus sequence by Multiple alignment
> taking only those 5 sequences (excluding our query
> seq) and then align that consensus sequence with our
> query sequence both at sequence level and structure
> level.
> I shall refine my doubt if am not clear in my
> subsequent discussions.Thanks in advance
> 
> Ayyagari Kiran 
>  
> 
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=====
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