Cite as: Cold Spring Harb. Protoc.; 2009; doi:10.1101/pdb.top43

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 Similar articles in PubMed
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 PubMed Citation
Right arrow Articles by Mount, D. W.
Related Collections
Right arrow Bioinformatics/Genomics, general
Right arrow Alignment of Sequences
Right arrow Alignment of Sequences, general
Right arrow Multiple Sequence Alignment
Right arrow Computational Biology
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?

topic_introductionTopic Introduction

Using Progressive Methods for Global Multiple Sequence Alignment

David W. Mount

Adapted from Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. CSHL Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

Finding a global optimal alignment of more than two sequences that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time is especially difficult. The dynamic programming algorithm used for optimal alignment of pairs of sequences can be extended to global alignment of three sequences, but for more than three sequences, only a small number of relatively short sequences may be analyzed. Thus, approximate methods are used for global sequence alignment. One class of these methods is progressive global alignment, which starts with an alignment of the most alike sequences and then builds an alignment by adding more sequences. This article introduces three programs that use progressive alignment methodology.


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

Comparing Programs and Methods to Use for Global Multiple Sequence Alignment
David W. Mount
Cold Spring Harb Protoc 2009: 61. [Abstract] [Full Text]

Using Hidden Markov Models to Align Multiple Sequences
David W. Mount
Cold Spring Harb Protoc 2009: 41. [Abstract] [Full Text]

Using Iterative Methods for Global Multiple Sequence Alignment
David W. Mount
Cold Spring Harb Protoc 2009: 44. [Abstract] [Full Text]

Using Multiple Sequence Alignment Editors and Formatters
David W. Mount
Cold Spring Harb Protoc 2009: 45. [Abstract] [Full Text]

Maximum Parsimony Method for Phylogenetic Prediction
David W. Mount
Cold Spring Harb Protoc 2008: 32. [Abstract] [Full Text]

Distance Methods for Phylogenetic Prediction
David W. Mount
Cold Spring Harb Protoc 2008: 33. [Abstract] [Full Text]

The Maximum Likelihood Approach for Phylogenetic Prediction
David W. Mount
Cold Spring Harb Protoc 2008: 34. [Abstract] [Full Text]



This article has been cited by other articles:


Home page
 Cold Spring Harb ProtocHome page
D. W. Mount
Comparing Programs and Methods to Use for Global Multiple Sequence Alignment
Cold Spring Harb Protoc, July 1, 2009; 2009(7): pdb.ip61 - pdb.ip61.
[Abstract] [Full Text]

Home page
 Cold Spring Harb ProtocHome page
D. W. Mount
Using Hidden Markov Models to Align Multiple Sequences
Cold Spring Harb Protoc, July 1, 2009; 2009(7): pdb.top41 - pdb.top41.
[Abstract] [Full Text]

Home page
 Cold Spring Harb ProtocHome page
D. W. Mount
Using Iterative Methods for Global Multiple Sequence Alignment
Cold Spring Harb Protoc, July 1, 2009; 2009(7): pdb.top44 - pdb.top44.
[Abstract] [Full Text]

Home page
 Cold Spring Harb ProtocHome page
D. W. Mount
Using Multiple Sequence Alignment Editors and Formatters
Cold Spring Harb Protoc, July 1, 2009; 2009(7): pdb.top45 - pdb.top45.
[Abstract] [Full Text]