Cite as: Cold Spring Harb. Protoc.; 2007; doi:10.1101/pdb.ip40

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Recommended Steps for a FASTA 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

The following strategy is recommended for searches with FASTA for finding the most homologous sequences in a database search while avoiding false-negative matches.


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D. W. Mount
Studies of Varying Alignment Algorithm, Amino Acid Scoring Matrix, and Gap Penalties
CSH Protocols, June 1, 2008; 2008(7): pdb.ip60 - pdb.ip60.
[Abstract] [Full Text]