A novel method for GPCR recognition and family classification from sequence alone using signatures derived from profile hidden Markov models.
نویسندگان
چکیده
G-protein coupled receptors (GPCRs) constitute a broad class of cell-surface receptors, including several functionally distinct families, that play a key role in cellular signalling and regulation of basic physiological processes. GPCRs are the focus of a significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs, whereas they still comprise the best potential targets for drug design. Taking into account the excess of data derived by genome sequencing projects, the use of computational tools for automated characterization of novel GPCRs is imperative. Typical computational strategies for identifying and classifying GPCRs involve sequence similarity searches (e.g. BLAST) coupled with pattern database analysis (e.g. PROSITE, BLOCKS). The diagnostic method presented here is based on a probabilistic approach that exploits highly discriminative profile Hidden Markov Models, excised from low entropy regions of multiple sequence alignments, to derive potent family signatures. For a given query, a P-value is obtained, combining individual hits derived from the same family. Hence a best-guess family membership is depicted, allowing GPCRs' classification at a family level, solely using primary structure information. A web-based version of the application is freely available at URL: http:/bioinformatics.biol.uoa.gr/PRED-GPCR.
منابع مشابه
Improving Phoneme Sequence Recognition using Phoneme Duration Information in DNN-HSMM
Improving phoneme recognition has attracted the attention of many researchers due to its applications in various fields of speech processing. Recent research achievements show that using deep neural network (DNN) in speech recognition systems significantly improves the performance of these systems. There are two phases in DNN-based phoneme recognition systems including training and testing. Mos...
متن کاملA Sensor-Based Scheme for Activity Recognition in Smart Homes using Dempster-Shafer Theory of Evidence
This paper proposes a scheme for activity recognition in sensor based smart homes using Dempster-Shafer theory of evidence. In this work, opinion owners and their belief masses are constructed from sensors and employed in a single-layered inference architecture. The belief masses are calculated using beta probability distribution function. The frames of opinion owners are derived automatically ...
متن کاملMultiple alignment and multiple sequence based searches
Multiple sequence alignments reveal patterns of conservation that can be exploited in database searches using “profile” methods. Starting with a single nematode sequence that has no informative BLAST hits, I give a real example of the use of multiple alignment and profile search software to detect informative remote homologies. It used to be that most new sequences were novel, with no informati...
متن کاملA Bayesian network model for protein fold and remote homologue recognition
MOTIVATION The Bayesian network approach is a framework which combines graphical representation and probability theory, which includes, as a special case, hidden Markov models. Hidden Markov models trained on amino acid sequence or secondary structure data alone have been shown to have potential for addressing the problem of protein fold and superfamily classification. RESULTS This paper desc...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- SAR and QSAR in environmental research
دوره 14 5-6 شماره
صفحات -
تاریخ انتشار 2003