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protein/DNA sequence alignment tool

protein/DNA sequence alignment tool - Bioinformatics

protein/DNA sequence alignment tool - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 08-27-2009, 02:28 AM
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Default protein/DNA sequence alignment tool



can anybody please help me with the understanding of various algorithms used in the analysis of protein/DNA sequence alignment, in general?

what are the various algorithms commonly used ?
What all data base these algorithms use to generate data? I mostly work with human and mouse samples.

Thanks for the help!
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Old 09-02-2009, 02:33 AM
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Default Re: protein/DNA sequence alignment tool

Well there 2types:
1.local (Smith-waterman algorithm): Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith-Waterman algorithm is a general local alignment method also based on dynamic programming. With sufficiently similar sequences, there is no difference between local and global alignments.

2.global(Needleman-Wunsch algorithm):Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. (This does not mean global alignments cannot end in gaps.) A general global alignment technique is the Needleman-Wunsch algorithm, which is based on dynamic programming.

u also have the pairwise (comparison of 2 sequences)and Multiple sequence alignment(comparison of more than 2 sequences)
just search on the web.. you have many resources like: NCBI,EBI,DDBJ,etc.
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