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.


smith-waterman algo.

smith-waterman algo. - Bioinformatics

smith-waterman algo. - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


Reply
 
LinkBack Thread Tools Display Modes
  #1  
Old 12-26-2011, 09:39 PM
Pipette Filler
Points: 506, Level: 10 Points: 506, Level: 10 Points: 506, Level: 10
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2011
Posts: 20
Thanks: 0
Thanked 0 Times in 0 Posts
Default smith-waterman algo.



hi,
who can provide me with smith-waterman algo.? i don't need just score but need the algo. display the alignment between two sequences

thanks in advance
Reply With Quote
  #2  
Old 12-27-2011, 06:23 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: smith-waterman algo.

Do you need to display all possible local alignments for 2 sequence in a single view?

Or review every SW result local alignment in a separate view?
Reply With Quote
  #3  
Old 12-28-2011, 05:38 PM
Pipette Filler
Points: 506, Level: 10 Points: 506, Level: 10 Points: 506, Level: 10
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2011
Posts: 20
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: smith-waterman algo.

thanks,
I mean I want the output of algorithm be just the optimal (best)alignment between two sequences.

I want the algorithm , then I can write it in matlab code, because I did not find ready code. I have to write it , in matlab there is ready code for biological seq only.
Reply With Quote
  #4  
Old 12-29-2011, 08:27 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: smith-waterman algo.

Are you sure that you need SW but not Needleman–Wunsch algorithm to compare 2 sequences?

If you need local<->local alignment (that is SW), just run SW algorithm from within UGENE sequence viewer and sort results by score qualifier. The first one will be the best possible.
Reply With Quote
  #5  
Old 12-29-2011, 01:15 PM
Pipette Filler
Points: 506, Level: 10 Points: 506, Level: 10 Points: 506, Level: 10
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2011
Posts: 20
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: smith-waterman algo.

yes, i have neeleman-wunsch alg. ,but i need smith-waterman alg.

i don't need use UGENE, need the code so I can optimize it using particle swarm opt.

thanks
Reply With Quote
  #6  
Old 12-30-2011, 06:56 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: smith-waterman algo.

there are a lot of code samples around.

For example, AFAIR at least UGENE sources contain:
1) simple C++ SW implementation
2) SSE based SW implementation
3) CUDA based SW implementation
4) OpenCL based SW implementation

+ actually I would propose writing the code by yourself and check the versions above just as an optimization reference. In this case you will manage to optimize the algorithm for your needs more efficiently
Reply With Quote
  #7  
Old 12-31-2011, 01:12 PM
Pipette Filler
Points: 506, Level: 10 Points: 506, Level: 10 Points: 506, Level: 10
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2011
Posts: 20
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: smith-waterman algo.

Quote:
Originally Posted by mfursov View Post
there are a lot of code samples around.

For example, AFAIR at least UGENE sources contain:
1) simple C++ SW implementation
2) SSE based SW implementation
3) CUDA based SW implementation
4) OpenCL based SW implementation

+ actually I would propose writing the code by yourself and check the versions above just as an optimization reference. In this case you will manage to optimize the algorithm for your needs more efficiently
thank u very much,
i will see the first one, because i know c++
sir, i roughly write it in matlab code, but did not get the correct result
where , one auther in this link:

[Only registered users see links. ]

gave the perl code, i don't know it but i try to convert it.
i think the above matrix in this link has error, i'm not sure .i said that because i run code on these strings ,but did not get this matrix correctly.
i got the first five rows correctly, but the three last arte error.
for ex. in cell(6,8) , i think the exact value is one instead of 0.
i hope to check it please and tell me, if it exact that is meaning i did not fully understand the work of alg.

many thanks
Reply With Quote
  #8  
Old 01-19-2012, 07:59 PM
Pipette Filler
Points: 506, Level: 10 Points: 506, Level: 10 Points: 506, Level: 10
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2011
Posts: 20
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: smith-waterman algo.

Hi mfursov,
I have finished design th local and global alignment successfully.
As you know these algorithms depended on dynamic programming that is not suitable with large database of sequence as my case , because have large complexity time.
Now, I want to know which best algorithm PSO or ACO with seq. alignment?
Please , if u have any information or paper regarding PSO or ACO with pairwise seq. , please provide me.
thanks
Reply With Quote
Reply

Tags
algo , smith-waterman , smithwaterman


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
For Sandra Smith about InfoRelation.com inforelationX Physics Forum 0 11-24-2004 08:54 AM
For Sandra Smith about InfoRelation.com ada Botany Forum 0 11-13-2004 11:48 AM
To David E. Smith Lcenacqy Physics Forum 4 06-11-2004 02:59 AM
John Maynard Smith gestorben Michael Schuerig Forum Biologie 0 04-26-2004 07:07 PM


All times are GMT. The time now is 12:04 AM.


Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.15511 seconds with 16 queries