Go Back   Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum > Molecular Research Topics Forum > Bioinformatics
Register Search Today's Posts Mark Forums Read

Bioinformatics Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


HMM Algorithm for Multiple Sequence Alignment using SAM method

HMM Algorithm for Multiple Sequence Alignment using SAM method - Bioinformatics

HMM Algorithm for Multiple Sequence Alignment using SAM method - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


Reply
 
LinkBack Thread Tools Display Modes
  #1  
Old 02-16-2009, 06:33 AM
Pipette Filler
Points: 2, Level: 1 Points: 2, Level: 1 Points: 2, Level: 1
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Feb 2009
Posts: 0
Thanks: 0
Thanked 0 Times in 0 Posts
Question HMM Algorithm for Multiple Sequence Alignment using SAM method



hi can anyone give suggestions hw to use hmm based algorithm for multiple sequence alignment using SAM method

Last edited by admin; 02-17-2009 at 12:00 AM.
Reply With Quote
  #2  
Old 02-17-2009, 08:55 AM
Volunteer
Points: 2,219, Level: 30 Points: 2,219, Level: 30 Points: 2,219, Level: 30
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Feb 2009
Posts: 36
Thanks: 0
Thanked 10 Times in 10 Posts
Default Re: HMM Algorithm for Multiple Sequence Alignment using SAM method

Hi,
both SAM and HMMER algorithms could be used to compute sequence-to-sequence score.

AFAIK neither SAM nor HMMER are not tools for multiple alignment construction, so they do not provide any theory of how to do it. So this an open subject to research without definite solution.

A long time ago HMMER1 package had a tool named 'hmmt'. Here what Eddy wrote in his guide about it:

----------
Can I build a model from unaligned sequences? In principle, profile HMMs can be trained
from unaligned sequences; however, this functionality is temporarily withdrawn from HMMER. I recommend CLUSTALW as an excellent, freely available multiple sequence alignment program.
The original hmmt profile HMM training program from HMMER 1 is also still available, from
ftp://ftp.genetics.wustl.edu/pub/edd...er-1.8.4.tar.Z
-------

And here the link to the manual to this tool: [Only registered users see links. ]

After you have HMM profile built you can align any number of sequences to it one by one and get multiple alignment.
Reply With Quote
The Following User Says Thank You to mfursov For This Useful Post:
admin (02-17-2009)
Reply

Tags
algorithm , alignment , hmm , method , multiple , sam , sequence


Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Human Cytome Project - Update 24 Jan. 2005 Peter Van Osta Cell Biology and Cell Culture 1 08-01-2010 02:18 PM
Human Cytome Project - an idea - Update 19 April 2005 Peter Van Osta Cell Biology and Cell Culture 1 06-01-2009 02:17 PM
Sequence alignment from BLAST output Mark Nance Protocols and Methods Forum 1 09-17-2008 05:41 AM
A Human Cytome Project - an idea - Update 14 March 2005 Peter Van Osta Cell Biology and Cell Culture 0 03-14-2005 02:27 PM
Human Cytome Project - Update 6 Jan. 2005 Peter Van Osta Cell Biology and Cell Culture 0 01-06-2005 11:18 AM


All times are GMT. The time now is 12:11 PM.


Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.17682 seconds with 16 queries