On Mon, Jul 6, 2009 at 9:41 AM,
<modeller_usage-request@salilab.org> wrote:
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Today's Topics:
1. regarding multiple sequence alignment (shilpi)
2. Re: regarding multiple sequence alignment (Modeller Caretaker)
3. Re: resuming a crashed job (Modeller Caretaker)
4. Modeling large protein sequence having homologues with less
similarity. (Sehrish Batool)
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Message: 1
Date: Wed, 1 Jul 2009 14:33:12 +0200
From: shilpi <shilpi.chaurasia@gmail.com>
Subject: [modeller_usage] regarding multiple sequence alignment
To: modeller_usage@salilab.org
Message-ID:
<eba7cb770907010533x208c0fc1j61dd26ee85ad7ed3@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
I have aligned three homologous protein sequences by
salign_profile_profile.py , but the alignment file obtained is not accurate.
Can anyone tell me which script should I use for multiple sequence
alignment.
thanks
Shilpi
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Message: 2
Date: Wed, 01 Jul 2009 10:05:46 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] regarding multiple sequence alignment
To: shilpi <shilpi.chaurasia@gmail.com>
Cc: modeller_usage@salilab.org
Message-ID: <4A4B976A.9070003@salilab.org>
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On 07/01/2009 05:33 AM, shilpi wrote:
> I have aligned three homologous protein sequences by
> salign_profile_profile.py , but the alignment file obtained is not
> accurate. Can anyone tell me which script should I use for multiple
> sequence alignment.
That is not surprising - profile-profile alignment aligns two blocks of
previously-aligned sequences (two profiles). For example,
salign_profile_profile.py in the Modeller examples/salign/ directory
aligns two profiles read from mega_prune.faa; the first contains 15
sequences (align_block=15) and the second contains the remaining
sequences from mega_prune.faa.
For multiple alignment, if you have structures, use salign_multiple.py
or salign_iterative.py. If you only have sequences, either use malign or
modify the salign parameters in your existing script - at a minimum you
need to change align_what='BLOCK', alignment_type='TREE' and
similarity_flag=False, and remove align_block.
Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Thu, 02 Jul 2009 08:18:59 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re: [modeller_usage] resuming a crashed job
To: S?ren Skovstrup Hansen <ssk@farma.ku.dk>
Cc: modeller_usage@salilab.org
Message-ID: <4A4CCFE3.5010105@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1
S?ren Skovstrup Hansen wrote:
> A very simple question: Is it possible to resume a crashed Modeller job?
> I was running a more or less standard automodel job, but my computer
> crashed after building 200 out of 250 models. Hence, is it possible to
> resume this job and thereby evaluating and ranking all 250 build models
> via e.g. the DOPE score?
There is no automatic method. To get the remaining 50 models, you could
simply modify your Python script and rerun it (set
a.starting_model=201). You can extract the DOPE scores from the logfile
of the original run - but if you don't have that, you can recalculate
the scores using a script similar to that at
http://salilab.org/modeller/9v7/manual/node242.html
Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Mon, 6 Jul 2009 00:27:59 -0700 (PDT)
From: Sehrish Batool <sehrish_batool.bsbi@yahoo.com>
Subject: [modeller_usage] Modeling large protein sequence having
homologues with less similarity.
To: modeller_usage@salilab.org
Message-ID: <78887.24185.qm@web111114.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
?
???????? My target sequence of protein is too large containing more than 1000 amino acids and I found 4 homologues in PDB showing very less similarity?i-e. two showing 28% similarity, one?showing 24% and last?one showing 19% similarity with my target sequence. Also the starting residues of templates have no homology with my target sequence and Modeller?has to?read from 1st residue of template, that bocomes impossible in this case. So?now how?can I?model my target sequence???
?
???????
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