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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.

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.

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.

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

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:

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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.

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