Cite as: Cold Spring Harb. Protoc.; 2007; doi:10.1101/pdb.top15

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topic_introductionTopic Introduction

Strategies for Sequence Similarity Database Searches

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

Database similarity search programs tend to produce large volumes of output. It can become difficult to screen this volume of material and to assess whether the more remotely related sequences are really related to the query sequence. Thus, it is important to limit the sequence output; there are some relatively simple procedures that may be followed for each program, as described in this article. For searches of protein databases, avoid repetitive alignments with the same sequence by limiting searches to the protein sequence databases that are well curated, such as SwissProt and PIR, or to a specific genome, as opposed to the entire set of translated GenBank sequences (the GenPept database).


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Using PAM Matrices in Sequence Alignments
CSH Protocols, June 1, 2008; 2008(7): pdb.top38 - pdb.top38.
[Abstract] [Full Text]