Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Pietro Roversi]

Dear Manoj,

I usually utilize SALIGN to produce structure-based sequence alignments:

https://modbase.compbio.ucsf.edu/salign/

Ciao

Pietro

On 02-03-2023 08:45, Manoj N wrote:

Dear all,

We want to generate a structure-based multiple
sequence alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj

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Dr. Pietro Roversi, PhD
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Adjunct Lecturer in Mathematical Modeling for Biology
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Email: pietro.rove...@unimi.it
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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Harry Powell]

Hi Manoj

If the structures are in the PDB, then PDB-KB may have already done the work 
for you - 

https://www.ebi.ac.uk/pdbe/pdbe-kb/

They run Gesamt on homologous structures for the whole PDB every week (as I 
understand it).

Harry

> On 2 Mar 2023, at 07:45, Manoj N  wrote:
> 
> Dear all,
> We want to generate a structure-based multiple sequence 
> alignment for a large number of homologous structures (>100). 
> 
> What are the available programs (stand-alone or webserver) to do this? 
> 
> Thank you,
> Best wishes,
> Manoj
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Irwin Selvam]

Hi,

Have you tried GESAMT? See 
https://www.ccp4.ac.uk/html/gesamt.html#command-line-options

All the best,

Irwin

From: CCP4 bulletin board  on behalf of Manoj N 

Sent: Thursday, March 2, 2023 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Tools for structure-based multiple sequence alignment


Dear all,

We want to generate a structure-based multiple sequence 
alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj



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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Rigden, Dan]

Dear Manoj

I would recommend CCP4's own GESAMT for this.

Dan

Sent from Outlook for Android<https://aka.ms/AAb9ysg>

From: CCP4 bulletin board  on behalf of Manoj N 

Sent: Thursday, March 2, 2023 7:45:39 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Tools for structure-based multiple sequence alignment


Dear all,

We want to generate a structure-based multiple sequence 
alignment for a large number of homologous structures (>100).


What are the available programs (stand-alone or webserver) to do this?


Thank you,

Best wishes,

Manoj



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[ccp4bb] Tools for structure-based multiple sequence alignment

[Manoj N]

Dear all,
                We want to generate a structure-based multiple sequence alignment for a large number of homologous structures (>100).




What are the available programs (stand-alone or webserver) to do this? 



Thank you,
Best wishes,
Manoj








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