Cite as: Cold Spring Harb. Protoc.; 2009; doi:10.1101/pdb.top45

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 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?
Legend icon

topic_introductionTopic Introduction

Using Multiple Sequence Alignment Editors and Formatters

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

Sequence alignment editors enable the user to manually edit a multiple sequence alignment (msa) in order to obtain a more reasonable or expected alignment. Editors allow sequences to be reordered and/or modified using the computer’s cut and paste commands. They are designed to accept various msa formats and to provide the output file in a suitable user-designated format. Sequence formatters provide various output formatting options, such as color and shading schemes to enhance visualization of residue alignments. The formatters can output files in Postscript, EPS, RTF, and other widely recognized formats, while accepting the standard input formats, such as MSF, ALN, and FASTA. This article introduces a number of sequence alignment editors and formatters, and provides links to sites where they can be found.


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
CSH Protocols 2009: 61. [Abstract] [Full Text]

Using Hidden Markov Models to Align Multiple Sequences
David W. Mount
CSH Protocols 2009: 41. [Abstract] [Full Text]

Using Progressive Methods for Global Multiple Sequence Alignment
David W. Mount
CSH Protocols 2009: 43. [Abstract] [Full Text]

Using Iterative Methods for Global Multiple Sequence Alignment
David W. Mount
CSH Protocols 2009: 44. [Abstract] [Full Text]



This article has been cited by other articles:


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

Home page
 CSH ProtocolsHome page
D. W. Mount
Using Hidden Markov Models to Align Multiple Sequences
CSH Protocols, July 1, 2009; 2009(7): pdb.top41 - pdb.top41.
[Abstract] [Full Text]

Home page
 CSH ProtocolsHome page
D. W. Mount
Using Progressive Methods for Global Multiple Sequence Alignment
CSH Protocols, July 1, 2009; 2009(7): pdb.top43 - pdb.top43.
[Abstract] [Full Text]

Home page
 CSH ProtocolsHome page
D. W. Mount
Using Iterative Methods for Global Multiple Sequence Alignment
CSH Protocols, July 1, 2009; 2009(7): pdb.top44 - pdb.top44.
[Abstract] [Full Text]