SuiteMSA

Visual tools for multiple sequence alignment comparison and molecular sequence simulation

Catherine L. Anderson, Cory L. Strope, Etsuko Moriyama

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily.Results: We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs.Conclusions: SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.

Original languageEnglish (US)
Article number184
JournalBMC bioinformatics
Volume12
DOIs
StatePublished - May 21 2011

Fingerprint

Multiple Sequence Alignment
Sequence Alignment
Simulation
Computational Biology
Bioinformatics
Simulator
Simulators
Alignment
Vision
Evaluate
Phylogeny
Graphical User Interface
Research
Inconsistent
Java
Graphical user interfaces
Research Personnel
Statistics
Series

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

SuiteMSA : Visual tools for multiple sequence alignment comparison and molecular sequence simulation. / Anderson, Catherine L.; Strope, Cory L.; Moriyama, Etsuko.

In: BMC bioinformatics, Vol. 12, 184, 21.05.2011.

Research output: Contribution to journalArticle

@article{3170ededb824437a9263786e7c70c9f0,
title = "SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation",
abstract = "Background: Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily.Results: We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs.Conclusions: SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.",
author = "Anderson, {Catherine L.} and Strope, {Cory L.} and Etsuko Moriyama",
year = "2011",
month = "5",
day = "21",
doi = "10.1186/1471-2105-12-184",
language = "English (US)",
volume = "12",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",

}

TY - JOUR

T1 - SuiteMSA

T2 - Visual tools for multiple sequence alignment comparison and molecular sequence simulation

AU - Anderson, Catherine L.

AU - Strope, Cory L.

AU - Moriyama, Etsuko

PY - 2011/5/21

Y1 - 2011/5/21

N2 - Background: Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily.Results: We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs.Conclusions: SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.

AB - Background: Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily.Results: We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs.Conclusions: SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.

UR - http://www.scopus.com/inward/record.url?scp=79956190847&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79956190847&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-12-184

DO - 10.1186/1471-2105-12-184

M3 - Article

VL - 12

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

M1 - 184

ER -