| | 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.