Pick one of the predicted genes from Exercise 1 and locate it in the human genome:
You may follow the directions for finding a gene by name or by protein sequence in Ensembl , and use at least one other genome sites as well:
Question 1: Is the annotation consistent among the various genome browsers?
Question 2: Is your gene in the same location/chromosome region/arm in these genome browsers?
Question 3: What other information can you extract from the genomebrowsers regarding your gene?
Prediction of Physical Properties
Compute pI/MW http://www.expasy.ch/tools/pi_tool.html
MOWSE http://srs.hgmp.mrc.ac.uk/cgi-bin/mowse
PeptideMass http://www.expasy.ch/tools/peptide-mass.html
TGREASE ftp://ftp.virginia.edu/pub/fasta/
SAPS http://www.isrec.isb-sib.ch/software/SAPS_form.html
Prediction of Protein Identity Based on Composition
AACompIdent http://www.expasy.ch/tools/aacomp/
AACompSim http://www.expasy.ch/tools/aacsim/
PROPSEARCH http://www.embl-heidelberg.de/prs.html
Motifs and Patterns
BLOCKS http://blocks.fhcrc.org
Pfam http://www.sanger.ac.uk/Software/Pfam/
PRINTS http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/PRINTS.html
ProfileScan http://www.isrec.isb-sib.ch/software/PFSCANform.html
Prediction of Secondary Structure and Folding Classes
nnpredict http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html
UCLA-DOE http://fold.doe-mbi.ucla.edu/
SWISS-MODEL http://www.expasy.ch/swissmod/SWISS-MODEL.html
PredictProtein http://www.embl-heidelberg.de/predictprotein/
Jpred http://www.compbio.dundee.ac.uk/~www-jpred/
PSIPRED http://bioinf.cs.ucl.ac.uk/psipred
PREDATOR (no longer available as as web server) http://www.embl-heidelberg.de/predator/predatorinfo.html