SAM-T2K and support vector machine GPCR predictions
taken from Affymetrix
Lists of known genes predicted peptides
Here are the results of screening a list of Affymetrix known genes and a list of Affymetrix gene predictions from the Oct. 7, 2000 freeze of the human genome for peptides which are strong hits to hidden Markov models built for Class A, Class B, Class C, and Frizzled/Smoothened GPCRs. (Three of the remaining GPCR classes: Class D, Class E and Drosophila Odorant do not occur in humans, and the fourth: Ocular albinism proteins is too small for subfamily classification as it contains only two known members, one mouse and one human).
Each screening currently includes, for each genomic peptide sequence:
- HMM E-value (measure of statistical significance of the hit). The strongest hits have the lowest E-values.
- A link to a page containing subfamily predictions for the sequence made by a library of support vector machines trained on data from the GPCRDB information system. The subfamily predictions pages also contain direct links to information in GPCRDB and the U.C. Santa Cruz Human Genome Browser.
- A BLASTme button. This button will produce a list of the top ten NCBI-BLAST hits against the non-redundant protein database nr. The list includes alignments and a graphical representation of the aligned hits.
The screenings can also be viewed as tracks in the CMPS244 mirror version of the Human Genome Browser.
Frizzled/Smoothened GPCRs[known][predicted]
To get a subfamily prediction for a sequence you are interested in, visit the GPCR Subfamily Classifier