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  • Doonesbury mentions “Bioinformatics in Proteomics”…

    November 14th, 2010, 8:22 pm

    …so clearly we’ll all soon be famous. Or something.

    I wonder who the big star is?


    CPTI eProtein Newsletter Researcher Spotlight feature

    November 9th, 2010, 11:30 am

    My work, and links to my tools, have been featured in the clinical proteomics technology initiative (CPTI) eProtein newsletter, “Researcher Spotlight: Enabling the Search for Novel Cancer Protein Variants.” Check it out, and give the Peptide Sequence Database (PepSeqDB), Peptide Arbiter by Machine Learning (PepArML) Meta-Search Engine, and PeptideMapper tools a try.

    The PepSeqDB fasta sequence databases provide a comprehensive enumeration of (putative) peptide sequences from ESTs, mRNAs, and protein sequence databases for human, mouse, rat, and zebra-fish.

    The PepArML meta-search engine searches tandem mass-spectra against protein sequence databases (including PepSeqDB) using seven search engines (Mascot, Tandem, Tandem with K-Score and S-Score scoring plugins, OMSSA, Myrimatch, and InsPecT) and combines the search results using unsupervised machine-learning. This infrastructure typically identifies two-to-three times more spectra than individual search engines at 10% FDR.

    The PeptideMapper web-service provides real-time, one-click mapping of peptide sequences for human, mouse, or rat, to a genome annotation track of the UCSC genome browser, and onto their protein, mRNA, and genomic evidence. Peptides containing (coding) single nucleotide polymorphisms (SNPs) at also mapped, making it possible to evaluate cSNPs by their mass-delta, amino-acid substitution, and genomic context.