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fast GLOBAL alignment tool

fast GLOBAL alignment tool - Protocols and Methods Forum

fast GLOBAL alignment tool - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


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  #1  
Old 09-13-2003, 12:20 PM
Andrea
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Default fast GLOBAL alignment tool



Hi,
I am looking for a fast global alignment tool.
I want to find the most identical sequences by comparing a query
sequence with a sequence database.
If I do this with blast or fasta I will get local alignments only but
I want to have an alignment with the complete sequence.
Is there a tool like this?
As far as I know I have to use the Needleman-Wunsch algorithm for
this, am I right?

Thanks for your help!

Andrea
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  #2  
Old 09-13-2003, 04:42 PM
Dr. James J. Campanella
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Default fast GLOBAL alignment tool

Dear Andrea,

There is an journal article and new global alignment/similarity matrix
generating tool called MatGAT at the BMC Bioinformatics link below. It is
very flexible and should do what you want:

[Only registered users see links. ]

Good Luck,

Jim Campanella


At 08:20 AM 9/13/03, Andrea wrote:

James J. Campanella,
Asst. Professor
Department of Biology and Molecular Biology
Montclair State University
1 Normal Avenue
Montclair, NJ 07043

Alternate email address: [Only registered users see links. ]

Ph: 973-655-4097
Fax: 419-791-9834

---
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  #3  
Old 09-15-2003, 09:50 AM
Andrea
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Default fast GLOBAL alignment tool

Hi Jim,

thanks for this information!
Seems to be the thing I was looking for.

Regards,
Andrea


[Only registered users see links. ] ("Dr. James J. Campanella") wrote in message news:<5.2.0.9.0.20030913123641.0268e170@mail.montc lair.edu>...
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  #4  
Old 09-16-2003, 06:46 AM
Dr Engelbert Buxbaum
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Default fast GLOBAL alignment tool

Andrea wrote:


Have you looked at ClustalX? I have recently done an alignment with
almost 400 sequences of a 70 kDa protein, so it is definetly powerful.
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