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BIOINFORMATICS APPLICATIONS NOTE
Vol. 20 no. 3 2004, pages 426–427
DOI: 10.1093/bioinformatics/btg430
The Jalview Java alignment editor
Michele Clamp
1,2,4,∗
, James Cuff
1,2
, Stephen M. Searle
1,2
and Geoffrey J. Barton
2,3,4
1
The Wellcome Trust Sanger Institute and
2
The European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK,
3
School of Life Sciences,
University of Dundee, Dow St, Dundee, DD1 5EH, UK and
4
The Wellcome Trust Centre
for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
Received on April 16, 2003; revised on August 4, 2003; accepted on August 6, 2003
Advance Access Publication January 22, 2004
ABSTRACT
Summary: 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 editoris presented here, whichenablesfastviewing
and editing of large multiple sequence alignments.
Availability:TheJarfileandsourcecodeforJalviewisfreely
available via the World Wide Web at http://www.jalview.
org. A Jalview mailing list is also available by e-mailing
majordomo@sanger.ac.uk with subscribe Jalview in the body
of the mail.
Contact: michele@sanger.ac.uk
INTRODUCTION
The alignment of biological sequences has a long history and
the development of automatic techniques has eased the dif-
ficulty of generating alignments from unaligned sequences.
However, even the best multiple sequence alignment methods
only achieve <50% accuracy per position in the alignment
of sequences with <20% identity (Thompson et al., 1999).
Biologists can often use other information about the sequence
and structure of a family of proteins to improve a multiple
sequence alignment. Therefore, biologists striving for the
best possible alignment will often need to edit manually an
automatically generated alignment.
There exist a large number of software packages that allow
the viewing of multiple sequence alignments. These include
Belvu, Alscript (Barton, 1993), ClustalX (Thompson et al.,
1997) and Chroma (Goodstadt and Ponting, 2001). These
packages do not allow editing of multiple sequence align-
ments.Although alignments can be edited in word processing
∗
To whom correspondence should be addressed.
software, such as Microsoft Word or emacs, it is often
difficulttosee conservedpatterns without aspecificcolouring
of the alignment that these programs do not provide. In
addition, specialized multiple sequence alignment editors
can provide extra features for the user including group-
ing and analysis of the conservation patterns in the align-
ment. A small number of software packages exist that allow
editing of multiple sequence alignments, such as Gene-
Doc (Nicholas and Nicholas, 1997, http://www.cris.com/
~Ketchup/genedoc.shtml), BioEdit, Seaview (Galtier et al.,
1996), MPSA(Blanchetetal.,2000),ANTHEPROT(Deleage
et al., 2001) and CINEMA (Parry-Smith et al.,1998) amongst
others. Of these, CINEMA has most similarities with Jalview
as it is written in Java. However, Jalview provides extra func-
tionalitywiththeabilityto calculatetrees, conservationwithin
subfamilies and on the fly pairwise alignments.
The Jalview program was written with the following design
goals in mind. First, it should be platform independent;
second, it should be fast and capable of editing of large mul-
tiple sequence alignments without significant degradation of
performance; and third, it should allow multiple integrated
views of the alignment and other data. These goals were
addressed by coding the software in the platform independent
Java version 1.1 language.
FEATURES OF JALVIEW
Jalview has a rich functionality based on its core alignment
viewing and editing options. These features are described in
outline in the following section. Jalview can input and output
multiple sequence alignmentsin a variety ofcommon formats
includingMSF,aligned FastaandClustalformat. Onceloaded
into Jalview the alignments are coloured by default according
to the ClustalX colouring scheme (Thompson et al., 1997). A
number of other colouring options are available via the edit
menu including a user configurable scheme. If the user does
not have a sequence alignment, a set of unaligned sequences
can be aligned using ClustalW either locally or via the web at
the EBI ClustalW server (Brooksbank et al., 2003).
426 Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.
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Jalview Java alignment editor
Editing multiple sequence alignments in Jalview simply
requiresthe userto dragresidues totheleft toremovegapsand
to the right to insert gaps at the cursor position. Editing can
be carried out on multiple sequences by applyinggroup selec-
tion, foundintheeditmenu. Groupingsequencescanspeedup
editing of large numbers of similar sequences. Jalview allows
users to calculate UPGMA or neighbour-joining trees (Saitou
and Nei, 1987). Upon selecting this option, a new window
is opened to display the tree. These trees can be used to re-
orderthe sequences in a multiplealignmentas well as to select
groups of sequences for group editing.
Sequence features on a multiple sequence alignment can
be viewed in Jalview. If the sequence identifiers in the align-
ment are Swiss-Prot/TrEMBL identifiers Jalview can access
the EBI website via SRS to download feature table elements
and display them on the alignment (Brooksbank et al., 2003).
Byright-clickingonSwiss-Prot/TrEMBLsequenceidentifiers
in the alignment window, the entry is retrieved from an SRS
server and displayed in Jalview’s lightweight web-browser. If
a structure is knownfor one of the sequences inthe alignment,
thiscan alsobe downloadedfroman SRSserverand displayed
in the Jalview structure viewer. The colour scheme from the
alignment is projected on to the structure to highlight regions
of conservation.
Principal component analysis (PCA) can help in under-
standing the relationship between sequences of an alignment.
ThemethodofclusteringsequencesimplementedinJalviewis
based on the method applied in SequenceSpace (Casari et al.,
1995). When PCA is selected from the calculate menu a PCA
viewer window is created that shows the sequences projec-
ted on to the first three eigenvectors. Clicking on points in
the PCA window selects the corresponding sequence in the
alignment window and in the tree window if it is visible.
Multiple sequence alignments often contain sub-families of
sequences and applying a colour scheme across the whole
alignment can make it difficult to identify these families.
Jalview allows the user to define sequence groups easily by
using the tree panel. Clicking on the tree defines a max-
imum distance apart any two sequences can be in a group
and the alignment is split into groups accordingly. Conserva-
tion across each group can then be calculated by considering
the different amino acid properties across each column in the
group(Zvelebiletal.,1987). Columnsthataremostconserved
have the most intense colour schemes fading to no colouring
at all for unconserved columns.
The Jalview software was originally written in 1997 and
is now widely used with over 20 000 downloads. It has
been used to produce publication quality alignment figures
as well as to provide a platform independent method to view
multiple sequence alignments by databases, such as Pfam
(Bateman et al., 2002). Jalview is run as an applet via the
Pfam web pages, for an example see http://www.sanger.
ac.uk/Software/Pfam/cgi-bin/getacc.pl?PF00045. Jalview is
also used by the EBI ClustalW server (Brooksbank et al.,
2003) as well as in the Apollo genome annotation editor
(Lewisetal., 2002). The supplementary information available
at http://www.jalview.org/bioinf/supp.html includes a figure
showing a screenshot of the main Jalview windows.
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