Cite as: Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.top40

This Protocol
Right arrow Full Text
Right arrow Update/discuss this protocolDiscussion icon
Right arrow Alert me when this protocol is cited
Right arrow Alert me when comments are published
Right arrow Alert me if a correction is posted
Services
Right arrow Similar protocols in this database
Right arrow Alert me to new releases of protocols
Right arrow Save to Personal Folders
Right arrow Download to citation manager
Right arrow Printer-friendly versionPrinter-friendly version
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Mount, D. W.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Mount, D. W.
Related Collections
Right arrow Bioinformatics/Genomics, general
Right arrow Alignment of Sequences
Right arrow Alignment of Pairs of Sequences
Right arrow Computational Biology
Right arrow Genetics, general
Right arrow Proteins and Proteomics, general
Right arrow Proteomics
Right arrow Evolution
Right arrow Genome Analysis
Right arrowRelated Articles
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati   Add to Twitter  
What's this?
BSN globe

topic_introductionTopic Introduction

Using Gaps and Gap Penalties to Optimize Pairwise Sequence Alignments

David W. Mount

Adapted from "Alignment of Pairs of Sequences," Chapter 3, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

To obtain the best possible alignment between two sequences, it is necessary to include gaps in sequence alignments and use gap penalties. For aligning DNA sequences, a simple positive score for matches and a negative score for mismatches and gaps are most often used. To score matches and mismatches in alignments of proteins, it is necessary to know how often one amino acid is substituted for another in related proteins. In addition, a method is needed to account for insertions and deletions that sometimes appear in related DNA or protein sequences. To accommodate such sequence variations, gaps that appear in sequence alignments are given a negative penalty score reflecting the fact that they are not expected to occur very often. Mathematically speaking, it is very difficult to produce the best-possible alignment, either global or local, unless gaps are included in the alignment. This article discusses how to use gaps and gap penalties to optimize pairwise sequence alignments.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati   Add to Twitter Twitter    What's this?

Related Articles

A Test of the Markov Model of Evolution in Proteins
David W. Mount
CSH Protocols 2008: 58. [Abstract] [Full Text]

Comparison of the PAM and BLOSUM Amino Acid Substitution Matrices
David W. Mount
CSH Protocols 2008: 59. [Abstract] [Full Text]

Studies of Varying Alignment Algorithm, Amino Acid Scoring Matrix, and Gap Penalties
David W. Mount
CSH Protocols 2008: 60. [Abstract] [Full Text]

Using PAM Matrices in Sequence Alignments
David W. Mount
CSH Protocols 2008: 38. [Abstract] [Full Text]

Using BLOSUM in Sequence Alignments
David W. Mount
CSH Protocols 2008: 39. [Abstract] [Full Text]

Using a FASTA Sequence Database Similarity Search
David W. Mount
CSH Protocols 2007: 16. [Abstract] [Full Text]

Using the Basic Local Alignment Search Tool (BLAST)
David W. Mount
CSH Protocols 2007: 17. [Abstract] [Full Text]



This article has been cited by other articles:


Home page
 CSH ProtocolsHome page
D. W. Mount
A Test of the Markov Model of Evolution in Proteins
CSH Protocols, June 1, 2008; 2008(7): pdb.ip58 - pdb.ip58.
[Abstract] [Full Text]

Home page
 CSH ProtocolsHome page
D. W. Mount
Comparison of the PAM and BLOSUM Amino Acid Substitution Matrices
CSH Protocols, June 1, 2008; 2008(7): pdb.ip59 - pdb.ip59.
[Abstract] [Full Text]

Home page
 CSH ProtocolsHome page
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]

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

Home page
 CSH ProtocolsHome page
D. W. Mount
Using BLOSUM in Sequence Alignments
CSH Protocols, June 1, 2008; 2008(7): pdb.top39 - pdb.top39.
[Abstract] [Full Text]