De novo interpretation of tandem mass spectrometry (MS/MS) spectra provides sequences for searching protein databases when limited sequence information is present in the database. Our objective was to define a strategy for this type of homology-tolerant database search. Homology searches, using MS-Homology software, were conducted with 20, 10, or 5 of the most abundant peptides from 9 proteins,...

MOTIVATION Detecting homologous proteins is one of the fundamental problems in computational biology. Many tools to solve this problem have been developed, but development of a simple, effective and generally applicable method is still desirable. RESULTS We propose a simple but effective information retrieval approach, named SIMPRO, to identify homology relationship between proteins. The key ...

*Correspondence to: Stefan Jentsch; Email: [email protected] Submitted: 06/03/2013; Accepted: 06/05/2013 http://dx.doi.org/10.4161/cc.25836 Comment on: Renkawitz J, et al. Mol Cell 2013; 50:261-72; PMID:23523370; http://dx.doi.org/10.1016/j.molcel.2013.02.020 DNA double-strand breaks (DSBs) are one of the most toxic types of DNA damage, as their inaccurate repair results in mutations and c...

Detection of sequences that are homologous, i.e. descended from a common ancestor, is a fundamental task in computational biology. This task is confounded by low-complexity tracts (such as atatatatatat), which arise frequently and independently, causing strong similarities that are not homologies. There has been much research on identifying low-complexity tracts, but little research on how to t...