Please cite as: CSH Protocols; 2007; doi:10.1101/pdb.top16

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topic_introductionTopic Introduction

Using a FASTA Sequence Database Similarity Search

David W. Mount

Adapted from "Sequence Database Searching for Similar Sequences," Chapter 6, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

FASTA is a program for rapid alignment of pairs of protein and DNA sequences. Rather than comparing individual residues in the two sequences, FASTA searches for matching sequence patterns or words, called k-tuples. These patterns comprise k consecutive matches of letters in both sequences. The program then attempts to build a local alignment based on these word matches. Due to the ability of the algorithm to find matching sequences in a sequence database with high speed, FASTA is useful for routine database searches of this type. Comparable methods are the BLAST program, which is faster than FASTA, is of comparable sensitivity for protein queries, and also does DNA searches, and programs that use the Smith-Waterman dynamic programming algorithm for protein and DNA searches, which are slower but more sensitive when full-length protein sequences are used as queries.


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