The Jalview Java alignment editor

Michele Clamp (Lead / Corresponding author), James Cuff, Stephen M. Searle, Geoffrey J. Barton

Research output: Contribution to journalArticle

1103 Citations (Scopus)

Abstract

Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.

Original languageEnglish
Pages (from-to)426-427
Number of pages2
JournalBioinformatics
Volume20
Issue number3
Early online date22 Jan 2004
DOIs
Publication statusPublished - 12 Feb 2004

Fingerprint

Multiple Sequence Alignment
Sequence Alignment
Java
Alignment
Protein Sequence
Nucleic acids
Nucleic Acids
Databases
Proteins
Growth

Keywords

  • Algorithms
  • Database management systems
  • Documentation
  • Hypermedia
  • Information storage and retrieval
  • Sequence alignment
  • Sequence analysis, DNA
  • Software
  • User-computer interface
  • Word Processing

Cite this

Clamp, Michele ; Cuff, James ; Searle, Stephen M. ; Barton, Geoffrey J. / The Jalview Java alignment editor. In: Bioinformatics. 2004 ; Vol. 20, No. 3. pp. 426-427.
@article{5fc7f19f57b14c4f93965f285a31d80e,
title = "The Jalview Java alignment editor",
abstract = "Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.",
keywords = "Algorithms, Database management systems, Documentation, Hypermedia, Information storage and retrieval, Sequence alignment, Sequence analysis, DNA, Software, User-computer interface, Word Processing",
author = "Michele Clamp and James Cuff and Searle, {Stephen M.} and Barton, {Geoffrey J.}",
year = "2004",
month = "2",
day = "12",
doi = "10.1093/bioinformatics/btg430",
language = "English",
volume = "20",
pages = "426--427",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "3",

}

Clamp, M, Cuff, J, Searle, SM & Barton, GJ 2004, 'The Jalview Java alignment editor', Bioinformatics, vol. 20, no. 3, pp. 426-427. https://doi.org/10.1093/bioinformatics/btg430

The Jalview Java alignment editor. / Clamp, Michele (Lead / Corresponding author); Cuff, James; Searle, Stephen M.; Barton, Geoffrey J.

In: Bioinformatics, Vol. 20, No. 3, 12.02.2004, p. 426-427.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The Jalview Java alignment editor

AU - Clamp, Michele

AU - Cuff, James

AU - Searle, Stephen M.

AU - Barton, Geoffrey J.

PY - 2004/2/12

Y1 - 2004/2/12

N2 - Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.

AB - Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.

KW - Algorithms

KW - Database management systems

KW - Documentation

KW - Hypermedia

KW - Information storage and retrieval

KW - Sequence alignment

KW - Sequence analysis, DNA

KW - Software

KW - User-computer interface

KW - Word Processing

U2 - 10.1093/bioinformatics/btg430

DO - 10.1093/bioinformatics/btg430

M3 - Article

C2 - 14960472

VL - 20

SP - 426

EP - 427

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 3

ER -