LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase

Abstract

Compositional bias (i.e. a skew in the composition of a biological sequence towards a subset of residue types) can occur at a wide variety of scales, from compositional biases of whole genomes, down to short regions in individual protein and gene–DNA sequences that are compositionally biased (CB regions). Such CB regions are made from a subset of residue types that are strewn along the length of the region in an irregular way. Here, we have developed the database server LPS-annotate, for the analysis of such CB regions, and protein disorder in protein sequences. The algorithm defines compositional bias through a thorough search for lowest-probability subsequences (LPSs) (i.e., the least likely sequence regions in terms of composition). Users can (i) initially annotate CB regions in input protein or nucleotide sequences of interest, and then (ii) query a database of greater than 1 500 000 pre-calculated protein-CB regions, for investigation of further functional hypotheses and inferences, about the specific CB regions that were discovered, and their protein disorder propensities. We demonstrate how a user can search for CB regions of similar compositional bias and protein disorder, with a worked example. We show that our annotations substantially augment the CB-region annotations that already exist in the UniProt database, with more comprehensive annotation of more complex CB regions. Our analysis indicates tens of thousands of CB regions that do not comprise globular domains or transmembrane domains, and that do not have a propensity to protein disorder, indicating a large cohort of protein-CB regions of biophysically uncharacterized types. This server and database is a conceptually novel addition to the workbench of tools now available to molecular biologists to generate hypotheses and inferences about the proteins that they are investigating. It can be accessed at http://libaio.biol.mcgill.ca/lps-annotate.html.Database URL: http://libaio.biol.mcgill.ca/lps-annotate.html