Clustal omega

From: Jayashankar
Date: 27 March 2012 09:18

Dear All,

A bit offtopic question,

Does any body know how can I get the PIR output of the aligned sequence from clustal omega.
I have a full length protein solved, to give weightage during comparitive modelling, I use domains of the same/similar protein solved before.
I expect an alignment something that looks like one below, and clustalw does'nt seems to work , but clustal omega does it. But there is no .pir format output.


1.cccccccccccccaaaaaaaaaabbbbbbbb
2.-------------------------------------bbbbbbbb
3.ccccccccccccc------------------------------
4.------------------aaaaaaaaaaa--------------


Thanks
S.Jayashankar

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From: Tim Gruene

Dear S. Jayashankar,

have you tried the clustalw options '-convert -output=PIR'? This should
result in a pir-formatted output file.

Tim

- --
- --
Dr Tim Gruene

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From: Jayashankar

Dear Tim,

I try to model a full length protein based on various domains solved already.
In that case, alignment of multiple sequence should approximately locate to the corresponding domain region.

Clustalw results in an unexpected alignment file.
Whereas the output from clustal omega is perfect and the format what I need is not given in the output option.

Because I will be needing this .pir output file to model my target sequence using modeller.

thanks

S.Jayashankar

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From: Tim Gruene 

Dear Jayashankar,

sorry, you did explain this in your model and I flipped clustalo with
clustalw. Even though when I used the option '-convert', clustalw does
not re-align the input but simply converts it, so in case it can read
the clustalo output, this should do the job, shouldn't it?

Have you tried reading the output file with clustalx or seaview or
jalview? These programs should be able convert to various file formats
without messing up with the alignment.

Cheers,
Tim

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From: Jayashankar

Dear Tim,

Thanks, The Jalview, output to textbox in PIR worked thr trick.

S.Jayashankar