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EPipe 0.982 Server BETA version, return comments

The EPipe 0.982 server performs comparative analysis of protein sequences derived from the same transcript by alternative splicing, genome variation data (SNPs) or protein families from one or more organisms. The analysis is automated: the input proteins are first processed by a number of analysis and prediction methods, the results are then remapped onto a multiple alignment and compared. All the differences found between the variants are reported in detail. It is also possible to view the complete analysis and prediction results.

NOTE 1:   This service is under development; new analysis and prediction methods are being added, the output format is being refined etc. As many external tools are called special attention is given to the overall speed of the service. Documentation is in preparation.

NOTE 2:   EPipe is dependent on a number of other programs that have to be run on the input sequences prior to the comparative analysis. Therefore, the processing of multiple sequences may be time-consuming. In the case of prolonged wait the user is advised to use the e-mail option: at any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.

 Specify the input

 Input sequences

Paste a single or several amino acid sequences in FASTA format into the field below:

 or submit a file in FASTA format directly from your local disk:

 Multiple alignment

 Yes, let EPipe align the input sequences according to the settings below
 No, the input sequences are provided as an alignment

 Select features for analysis


In this section you select the features for your analysis. You can filter the features in Epipe by selecting the tag filters (blue boxes below) - they work with AND logic. Also you can add a keyword phrase to match the tool name or description. Use the button "Clear all filters" to reset all filters and show all features.


Clear all filters
Please note: The keyword filter is always applied (also when adjusting the filters buttons above).

To select a feature simply mark the checkbox to the left of the tool name in the table. You can also select and deselect the whole view in the table by clicking Select/Deselect shown below the table.
Please note: All features are alphabetically ordered with the selected features (in the current filter view selected above) at the top of the table.

Enabled

Name

Description


You can also paste in a quick feature selection string from a previous analysis in the field below and press apply to select all the features from the analysis (including any you might also have chosen).


Finally, you can save the current quick feature selection string for all the features currently selected by copying the string in the grey field below.




Restrictions:
At most 2,000 sequences and 200,000 amino acids per submission.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATION

For publication of results, please cite:

Protein annotation in the era of personal genomics.
Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S.
Curr Opin Struct Biol., 20:335-41, 2010.

EPipe 1.0: a pipeline for discovery of functional differences in proteins originating from alternative splicing, pan-genome variation or protein family evolution.
In preparation by several groups from the BioSapiens Network of Excellence, 2013.

The pipeline also relates to the work described in:

The implications of alternative splicing in the ENCODE protein complement.
Tress, ML et al.
Proc Natl Acad Sci U S A, 104:5495-5000, 2007.


GETTING HELP

Scientific issues:        Technical problems: