Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

List of Abstracts * Speakers * Organizers * Authors * Original Announcement

Computational Screening for Peroxisomal Proteins Using New Methods, Old Methods, and Human Expertise

Olof Emanuelsson1, Susana Cristobal2, Arne Elofsson1, Gunnar von Heijne1
1Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden 2Dept. of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
Telephone: +46-(0)8-55378574
Fax: +46-(0)8-55378214

The peroxisome is an important cellular compartment, responsible for carrying out many reactions essential to the organism. We have developed a sequence-based predictor as a part of an attempt to identify novel potential peroxisomal proteins (concentrating on the C-terminal PTS1 signal, -SKL). Our predictor was applied on seven eukaryotic genomes to find candidate proteins for peroxisomal localization, and the resulting initial set was further analyzed by phylogenetic profiling based on domain analysis using the Pfam database. Thus we were able to narrow down the set of potential peroxisomal proteins to a reasonably reliable set. Although more successful than other peroxisomal protein predictors publicly available, our method is also an illustration of the fact that some protein locations simply are harder to predict than other. In the peroxisomal case, this is largely accounted for by the low complexity of the PTS1 signal, making it hard to distinguish a PTS1 from similar or even identical motifs that do not target proteins to the peroxisome.

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List of Abstracts * Speakers * Organizers * Authors * Original Announcement

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