Task 3 - Sequence-based predictions 2011

In contrast to the vast amount of known protein sequences, information about structure and function is available for only very few proteins. Sequence-based predictions of protein features aim to decrease this gap.

Introductory talks

Talk on sequence feature prediction: Media:Talk_Task3.pdf

The talk introduced the prediction of:

• secondary structure
• disorder
• transmembrane helices and signal peptides
• GO terms

Tasks and questions

For each prediction, carry out these assignments and answer these questions:

• Collect basic information about the methods: author, year, reference
• Give a brief description of the theory and the algorithm, if possible
• What is predicted? Describe the features in some detail
• What information is required for the predictions?
• Apply the prediction methods to your protein and explain how to do this
• You may try out other protein sequences (this is required when specified)
• Present, describe and discuss the results
• Look for other methods, for example here: http://expasy.org/tools/
• You may try out more methods

1. Secondary structure prediction

PSIPRED

PSIPRED (with hints on running psipred locally)

• /apps/psipred_2.5 and psipred_3.2
• Script: runpsipred -> adapt paths
• Readme: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/
• Server: http://bioinf.cs.ucl.ac.uk/psipred/

Jpred3

Jpred3

• Server: http://www.compbio.dundee.ac.uk/www-jpred/index.html

Comparison with DSSP

DSSP

• /apps/dssp
• Server: http://swift.cmbi.ru.nl/servers/html/ (-> Protein analysis -> Secondary Structure, symmetry and accessibility)
• http://swift.cmbi.ru.nl/gv/dssp

2. Prediction of disordered regions

DISOPRED

DISOPRED (with hints on running psipred locally)

• /apps/disopred_2.4.2.
• Script: rundisopred -> adapt paths
• Server: http://bioinf.cs.ucl.ac.uk/disopred/

POODLE

• Server: http://mbs.cbrc.jp/poodle/poodle.html
• for example, POODLE-I (POODLE series only)

IUPRED

• Server: http://iupred.enzim.hu/index.html
• Try different prediction types

META-Disorder

• Do not run locally. If you are interested, have a look at "man metadisorder" in the VM
• You can use the PredictProtein server for the prediction

3. Prediction of transmembrane alpha-helices and signal peptides

• Predict transmembrane helices and signal peptides additionally for the following proteins: BACR_HALSA, RET4_HUMAN, INSL5_HUMAN, LAMP1_HUMAN and A4_HUMAN
• You can look for other alpha-helical transmembrane proteins and proteins with different signal peptides to apply the prediction methods
• Why is the prediction of transmembrane helices and signal peptides grouped together here?
• Describe different signal peptides

TMHMM

• in /apps/tmhmm-2.0c/bin: adapt paths in tmhmm, tmhmm.ORIG and tmhmmformat.pl (/usr/local/bin/ -> /usr/bin/)

Phobius and PolyPhobius

• Server: http://phobius.sbc.su.se/

OCTOPUS and SPOCTOPUS

• Server: http://octopus.cbr.su.se/index.php

SignalP

• in /apps/signalp-3.0/signalp: adapt path
• run as superuser

TargetP

• Server: http://www.cbs.dtu.dk/services/TargetP/

4. Prediction of GO terms

• Use also the additional proteins from the transmembrane/signal peptide prediction

GOPET

• Server: http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar

Pfam

• Database: http://pfam.sanger.ac.uk/ -> SEQUENCE SEARCH

ProtFun 2.2

• Server: http://www.cbs.dtu.dk/services/ProtFun/

TEST

line1 line2 line3

line4