Email address:
Your email address, to which the results
and a hyperlink of the results will be sent.
Address will not be verified, so ensure
the address is correct, or leave it blank.
SWISSPROT id:
If entered, the sequence will be fetched
from au.expasy.org in FASTA format, and
run through TMpro for transmembrane
helix predictions.
Browse:
Submit input sequence by uploading
the sequence file. Click browse and choose the file to be uploaded
and then press submit.
Raw Sequence:
If SWISSPROT id is empty, the text
in this box is saved and TMpro is run on this input.
Format options are raw sequence or
FASTA sequence. If FASTA sequence, it can include multiple
sequences (multiple sequence FASTA
format).
Notes:
Enter any text t hat you want
to save as notes for yourself for the submitted sequences. The notes
will be emailed back to you along
with results, so that you can keep track of what your submission is, etc
via the notes.
Clear:
Clear all the fields above.
Output:
For single sequence file (any format), the output
is generated into output.txt. The format is as follows:
Textual output
Line 1:
Header (obtained from FASTA/SWISSPROT
header, or generated). Line 2:
Resisdues Line 3, Line 4, Line 5, ....:
Out of the prediction,
one line per prediction type.
If the values are
binary, it indicates predicted TM regions--1 means TM residue, 0 means non
TM Residue
Each line has 5 fields:
Field one:
Description of contents of the line:
For example: TMpro NN Prediction with 0.4 as threshold and set 160 as training
set.
Field two:
Short legend key for the description
in Line 1: Example: TMpro (NN)
Field three:
IsBinary? If 1 it means, the values
are binary predictions (tm or nontm residue), If 0, means nonbinary, meaning
floating point
output from the prediction algo
Field four:
Values. These values are either (1)
amino acid residues or (2) binary predictions or (3) real values describing
corresponding
to each amino acid position, for example
probability that the residue is in transmembrane region, hydropathy value.
Graphical output
If you do not see the chart on pressing "Chart" button in output page, it is probably because Java Run time Environment is not installed on your computer.
Install Java Run Time Environment (JRE) to view interactive Chart. Text output can be seen without the JRE.
The output
is also shown as a graph.
Users can check/uncheck different graphs to show/nontshow
specific plots.
Special Options
User has an option to enter "known" helix positions (or
any other helix positions) so as to visualize predictions in
comparison to the values at user's
hands. User can enter # of known TM helices, and start and end position of
each helix.
This feature is also useful to compare
visually the predictions by different methods. User can input predicted helices
by other methods
and use the graphical
interface to compare the relative positions of helices predicted by different
methods
