Shannon Steinfadt

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One of the most commonly used tools by computational biologists is some form of sequence alignment. Heuristic alignment algorithms developed for speed and their multiple results such as BLAST [1] and FASTA [2] are not a total replacement for the more rigorous but slower algorithms like Smith- Waterman [3]. The different techniques complement one another. A(More)
Local sequence alignment is widely used to discover structural and hence, functional similarities between biological sequences. While the faster heuristic methods like BLAST and FASTA are useful to compare a single sequence to hundreds or even thousands of sequences in genetic databases such as GenBank, EMBL, and DDBJ, this work yields pairwise alignments(More)
More sensitive than heuristic methods for searching biological databases, the Smith-Waterman algorithm is widely used, but it has a high quadratic running time. This work presents a faster approach and implementation for Smith-Waterman that extends the traditional results to return multiple, BLAST-like sub-alignments. The extended Smith-Waterman using(More)
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