IMPORTANT: To use this
option you will need to input a sequence alignment. Please make sure
this alignment is in PIR or PHYLIP format. ALN and GCG MSF files are not
supported so you will have to convert your MSF files to PIR format with,
for example, GCG's ToPir:
topir pileup.msf{*} -outf=pileup.pir
Please refer to the GCG documentation to find out how to use this
program correctly. You may then use this file as input (cut and paste or
upload) to this service.
The method used is the NJ (Neighbour Joining) method of Saitou and
Nei. First you calculate distances (percent divergence) between all
pairs of sequence from a multiple alignment; second you apply the NJ
method to the distance matrix.
This option allows you to choose the following output formats for the
tree:
- Neighbour
- Phylip
- Distance
In order to view these trees you must
have a program capable of displaying the data. Please refer to this
pages section on OUTPUT
for more information.
- Kimura Correction of distances
This
options allows you to set on distances correction (correction for
multiple substitutions). This is because, as sequences diverge, more
than one substitution will happen at many sites. However, you only see
one difference when you look at the present day sequences. Therefore,
this option has the effect of stretching branch lengths in trees
(especially long branches). The corrections used here (for DNA or
proteins) are both due to Motoo Kimura.
- Ignore Gaps in alignment
With this
option, any alignment positions where ANY of the sequences have a gap
will be ignored. This means that 'like' will be compared to 'like' in
all distances. It also, automatically throws away the most ambiguous
parts of the alignment, which are concentrated around gaps (usually).
The disadvantage is that you may throw away much of the data if there
are many gaps.
- UPLOAD A FILE
You may upload a
file from your computer which containing a valid set of sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF,
Phylip or UniProt/Swiss-Prot) using this option. Please note
that this option only works with Netscape Browsers or Internet Explorer
version 5 or later. Some word processors may yield unpredictable results
as hidden/control characters may be present in the files. It is best to
save files with the Unix format option to avoid hidden windows
characters. Some examples of common sequence formats may be seen here.
- SCORES TABLE
Scores Table is a
new view to ClustalW output. Users can sort the scores by Alignment
Score, Sequence Number, Sequence Name and Sequence Length.
- REFERENCES
Higgins D.,
Thompson J., Gibson T. Thompson J. D., Higgins D. G., Gibson T.
J.(1994). CLUSTAL W: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting,position-specific
gap penalties and weight matrix choice. Nucleic Acids Res.
22:4673-4680. 
ClustalW WWW Service at the European
Bioinformatics Institute http://www.ebi.ac.uk/clustalw Rodrigo Lopez,
Services Program
Andrew Lloyd The Clustal W WW server at the
EBI embnet.news volume 4.2 1997 http://www.ebi.ac.uk/embnet.news/vol4_3/clustalw1.html
The
program in use in this service can be obtained freely from: http://www.sgi.com/chembio/resources/clustalw/parallel_clustalw.html
Parry-Smith, D.J., Payne, A.WR, Michie, A.D. and Attwood, T. K.
(1997) CINEMA - A novel Colour INteractive Editor for Multiple
Alignments. Gene, 211(2), GC45-56.  http://www.bioinf.man.ac.uk/dbbrowser/CINEMA2.1/
Attwood,
T. K., Payne, A. W.R., Michie, A.D. and Parry-Smith, D.J. (1997) A
Colour INteractive Editor for Multiple Alignments - CINEMA, EMBnet.news, 3 (3).
Jalview - a java
multiple alignment editor http://www.jalview.org
pfaat (Protein Family
Alignment Annotation Tool) http://pfaat.sourceforge.net/
- OTHER SERVICES:
This services
is also available as an application from the EBI's srs server: http://srs.ebi.ac.uk/
N.B. DbClustal can be launched from Wu-Blast2 and
NCBI-Blast2 you can choose some of the sequences
from your score list and align them with your query sequence. You may
also then paste your .aln files back into ClustalW (bootstrapping) in
order to colour
your alignments, view the phylogenetic
trees or launch jalview.
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