CLUSTALW
Enter or Paste a set of Sequences in any supported format.
All sequences must be in the same format :
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demo data
Clear
the data
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Upload Sequence file(upto 4.5 M)*
:
Advance Options :
KTUP(Word Size)
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1
2
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5
WINDOW LENGTH
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10
9
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6
5
4
3
2
1
PAIRGAP
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5
10
25
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500
MATRIX
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BLOSUM
PAM
GONNET
ID/option>
GAP OPEN
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100
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25
10
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1
END GAPS
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10
20
GAP Extension
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0.05
0.5
1.0
2.5
5.0
7.5
10.0
GAP Distances
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HELP :
KTUP(Word Size)
Top
This option allows you to choose which 'word-length' to use when calculating fast pairwise alignments.
WINDOW LENGTH
Top
Use this option to set the window length when calculating fast pairwise alignments.
Matrix
Top
This option allows you to choose which matrix series to use when generating the multiple sequence alignment. The program goes through the chosen matrix series, spanning the full range of amino acid distances.
* BLOSUM (Henikoff). These matrices appear to be the best available for carrying out data base similarity searches.
The matrix used is Blosum30. * PAM (Dayhoff). These have been extremely widely used since the late '70s. We use the PAM 350 matrix.
* GONNET. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set. They appear to be more sensitive than the Dayhoff series. We use the GONNET 250 matrix.
There is also an identity matrix which gives a score of 10 to two identical amino acids and a score of zero otherwise.
**Default matrix for proteins is Gonnet250.