Part A - Sequence and Choices
The first screen is composed of a window to insert the studied sequence (1),
three buttons to control
the software (2-4), three choices to control the type of predictions, eight for the outputs (5,6) and
one small text to see the advance of the computation (7).
- amino acid sequence
- copy the amino acid sequence in Fasta format.
NB: Fasta format is a simple format : (1) the first line is the name of the protein
beginning with a symbol ">" given ">name".
(2) The following lines are used for the amino acid sequence.
You could use the example button to see the example of protein 2aak.
- button submit
- When your sequence is written with your
prediction and output choices, just push this button.
The "state" will give you the state of the computation.
- clean button
- If you want to change your sequence, just push this button and everything in the window sequence
will be erased.
- protein 2 aak
- This protein was used in our paper as example (de Brevern AG., Etchebest C., and Hazout, S, Proteins, 2000). It is an alpha-beta protein.
You can download the 3D structure from the Protein Databank.
- type of predictions
- "Bayesian Prediction": the basic prediction is performed with one occurrence matrix per Protein Block.
- "Sequence Families" : a Bayesian prediction is performed with optimized matrices.
- "Sequence Families (new)" : the new approach has improved the prediction rate from 40.7% to 48.7%.
Each Protein Block could be characterized by several occurrence matrices, each one is associated with
a cluster of "related" amino acid sequences (increase the prediction accuracy for 95% to 99.8% of the proteins).
- Displaying of the results
- "Short results" : only the sequence
and the prediction in terms of Protein Blocks are given.
- "Results": normal results
are the same results than the previous item, but completed with
an index derived from the Neq to evaluate the prediction quality.
- "Complete results": the complete results are
the amino acid sequence, the prediction in terms of Protein Blocks
and the whole Protein Blocks with their associated probabilities.
- Neq information
- "Neq (Local)" : local Neq for every sites of the protein,
with the possibility to perform the two different strategies (local strategy and global strategy)
for a given prediction rate.
- "Neq (Global)" : global Neq for the complete protein,
with a rasmol script to visualize the informativity of the sequence directly on the structure
(if the 3D structure is available, click here
for more details).
- "All Neq Graphics" : The two last options.
- "Comparison [L]" : comparison between the prediction in terms of PBs and a 3D structure coded in terms of PBs.
- "Score visualisation" : The visualisation of the prediction scores (colored matrix).
- "All" : the two Neq graphics and the complete results.
- nothing special
- "State of LocPred : sleep " : no submission done.
- a wrong sequence
- "State of LocPred : no correct sequence " : too many errors in the sequence. So the prediction
could not be performed.
- too long sequence
- "Warning : sequence length too long" : only the beginning of the sequence is predicted.
Please cut the sequence into successive fragments. If you want a prediction for longer
sequence, cut your amino acid sequence into successive fragments (with overlaps).
The maximum length allowed is 2000 residues (mail me if you want a higher value by default).
- reading of the sequence
- "Sequence read" : no special problem to read the amino acid sequence.
- computation of Bayesian prediction
- "Bayesian Prediction in progress" : work in progress.
- "Bayesian Prediction done" : computation done.
- computation of Bayesian prediction with sequence families
- "Bayesian Prediction (Sequence Families) in progress" : work in progress.
- "Bayesian Prediction (Sequence Families) done" : computation done.
- "Short Results in progress" : frame for the short results option is in progress.
- "Results in progress" : frame for the (second) results option is in progress.
- "Complete Results in progress" : frame for the complete results option is in progress.
- "Computation done" : the work is done.
- "Neq (Local) in progress" : computation of local Neq is in progress.
- "Neq (Global) in progress" : computation of global Neq is in progress.
- "Computation done" : the work is done.
NB : The computation is always done in the same order (1) the results, (2) the local Neq, (3) the global Neq, (4) the comparison form and (5) the visualisation matrix.
- error messages
- If you see one please mail me (it's the message).
- "Finish" : everything is done. I hope our approach will help you, good luck.
Last modif : 11 April 2004