CBU - Computational Biology Unit

BOMP is a tool for prediction of beta-barrel integral outer membrane proteins (BOMPs). The user may submit a list of proteins, and receive a list of predicted BOMPs.

Send an email to webtools@bccs.uib.no

General instructions

To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially.

Typical running times:
1 protein: 10 seconds
10 proteins: 10 seconds
20 proteins: 10 seconds
100 proteins: 10 seconds
1000 proteins: 20 seconds
2000 proteins: 40 seconds

These running times are actually depending on how many integral outer membrane proteins that are predicted, so they will vary. An example with the predicted proteome of E.coli with 4346 proteins, takes around 45 seconds to process.

With BLAST turned on:
1 protein: 10 seconds
10 proteins: 15 seconds
20 proteins: 20 seconds
50 proteins: 50 seconds
100 proteins: 100 seconds
5000 proteins: 5000 seconds (~1.4 hrs)

These running times do not depend on how many proteins that are predicted to be integral outer membrane proteins.

This page is maintained by webmaster@bccs.uib.no. Last updated: Tuesday 12 February, 2008
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