Dear Thomas, You mentioned the free tools in details. I appreciate that. But what i don't understand is to manually call everyone, and then keep on doing it, is tedious but fun it is. I had a query that template secondary structure information is there in templates, but with indels, that may be disturbed. I mean the native information is deteriorated.

So if based on indels, available in current alignment, if i can link directly to a python script. So that my next programme to generate the optimal alignment will become successful, as i did all of these several times manually, to design the algorithm to generate best representative alignment.

Will you please elaborate this time.

Thanks, Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Friday, March 25, 2011 4:50:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 55

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Today's Topics:

1. How to get Secondary Structure in Alignment file (Ashish Runthala) 2. Re: How to get Secondary Structure in Alignment file (Thomas Evangelidis)

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Message: 1 Date: Fri, 25 Mar 2011 09:17:07 +0530 (IST) From: Ashish Runthala ashishr@bits-pilani.ac.in Subject: [modeller_usage] How to get Secondary Structure in Alignment file To: modeller modeller_usage@salilab.org Message-ID: 11283718.504161301024827590.JavaMail.root@mailserver.bits-pilani.ac.in Content-Type: text/plain; charset=utf-8

Dear Modellers, Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below

Template1> HCSIHISC Template2> HCSHHISC

H=Helix, C=Coil, S-Strand, I=Indels

Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds)

Thanks Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Message: 2 Date: Fri, 25 Mar 2011 13:20:42 +0200 From: Thomas Evangelidis tevang3@gmail.com Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file To: Ashish Runthala ashishr@bits-pilani.ac.in Cc: modeller modeller_usage@salilab.org Message-ID: AANLkTikYvKNM3qPUU4kJ=h50DE75AJS7ncZJqjMVPSdx@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

Maestro from Schrodinger can display both the predicted secondary structure elements (SSE) of the target and the SSE of the templates above the alignment dynamically (namely if you change the alignment the SSEs are changed accordingly).

Alternatively you can use the following commercial free tools:

ESPript (http://espript.ibcp.fr/ESPript/ESPript/): can create an image of your alignment with the SSEs of your templates above it. No SSE of the target is displayed though.

MolIDE (http://dunbrack.fccc.edu/molide/index.php): I have the notion that this alignment editor (and not only) can display both the predicted SSE of the target and the SSE of the templates. However, I didn't manage to run it yet due to compilation problems. I intend to give it a try in the near future.

STRAP (http://3d-alignment.eu/): it can do both but the GUI is not handy in Linux (windows and fonts are unequal, etc.).

Finally you can add a row with the secondary structure (as you wrote it in your email) above each sequence in your alignment editor. I prefer Jalview and like to play around with groups and colors. See the attached image for an example. SSE of your templates can be retrieved from PDB (e.g. http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=...) whereas the SSE of your target can be predicted by Jpred3 ( http://www.compbio.dundee.ac.uk/www-jpred/).

HTH,

Thomas

On 25 March 2011 05:47, Ashish Runthala ashishr@bits-pilani.ac.in wrote:

> Dear Modellers, > Suppose i have two templates, and a target sequence. Instead of sequence > alignment based file, i want to consider the secondary structure > information, like given below > > Template1> HCSIHISC > Template2> HCSHHISC > > H=Helix, C=Coil, S-Strand, I=Indels > > Is it possible to get the alignment in this case for multiple templates > against the target sequence( whose structure can also be represented as best > aligned folds) > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >