User Manual

0. Abstract

You can execute all process of ET(Evolutionary Trace) analysis in this server.
Beginning with your query sequence, you can finally see the trace residues mapped onto structure in PDBj Viewer.

You can back and re-calculate under another conditions through links at top of page.

1.Query Sequence

First you have to input amino acid sequece.

You can do this by following 5 forms.
(1)Input FASTA formatted text or simple text into text area
(2)Upload your file containing FASTA formatted text or simple text
(3)Upload your PDB file(In this case you can use this structure in later process.)
(4)Input PDB code and chain ID
(5)Input GI code

2.Condition of BLAST Search

First please confirm the sequence displayed.
We recommend "swissprot" as database, but if you cannot obtain enough sequence you should consider using "nr".

3.Result of BLAST and Selection of Sequences

Number of hit sequence is limited to 500.

Next you have to select sequences to use.
You can select sequences by each sequence's checkbox and by criteria of sequece idetity and coverage to the query sequence.
You can also create represetative sequence from selected sequences.

4.Result of Multiple Alignment and Condition of ET analysis

The result of multiple alignment is displayed.
If you find any sequences to be excluded from the analysis, click the sequence in phylogenetic tree or color map and exclude them in the popup window.
After that, please click "Re-Alignment" to re-calculate.

Condition of ET analysis is as below.
(1)Selection of sequence of your interest(usually Q(query) sequence). Gap sites in this sequence are ignored in the following analysis.

(2)Algorithm of ET. Real Value ET or Integer Value ET is recomennded.
(i)Read Value ET(ET with information entropy)
(ii)Integer Value ET(ordinary ET)
(iii)Entropy(This use only information entropy simply, doesnot use phylogenetic tree.)
(iv)Real Value ET(Zoom)(This use only classes containig sequence of your interest.)

(3)Coverage(ratio of trace residue to sequence length)

(4)Certain classification
You can specify certain classification point. If no, scores of all classification points are summed up.

(5)Accessible surface rate
A residue will be considered to be exposed or internal by this criteria.
When the analysis is done with the structure, internal residues are not considered to be trace residues.

(6)Clustering(condition for spatial clustering of trace residues)

(7)Selection of structure

(8)You can exclude residues contacted by other chains or ligands from trace residue.

5.Result of ET Analysis

Trace residues are colored red.
By clicking "Display TR on structure", you can see trace residues mapped onto structures and molecular surface colored according to score.
This function uses pdbjv, so installation of Java plugin and JOGL is required in advance.