Bernardes J, Zaverucha G, Vaquero C, Carbone A. Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.
PLoS Comput Biol 2016;
12:e1005038. [PMID:
27472895 PMCID:
PMC4966962 DOI:
10.1371/journal.pcbi.1005038]
[Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 06/28/2016] [Indexed: 11/30/2022] Open
Abstract
Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for annotation fail. Here we address the fundamental question of domain identification for highly divergent proteins. By using high performance computing, we demonstrate that the limits of state-of-the-art annotation methods can be bypassed. We design a new strategy based on the observation that many structural and functional protein constraints are not globally conserved through all species but might be locally conserved in separate clades. We propose a novel exploitation of the large amount of data available: 1. for each known protein domain, several probabilistic clade-centered models are constructed from a large and differentiated panel of homologous sequences, 2. a decision-making protocol combines outcomes obtained from multiple models, 3. a multi-criteria optimization algorithm finds the most likely protein architecture. The method is evaluated for domain and architecture prediction over several datasets and statistical testing hypotheses. Its performance is compared against HMMScan and HHblits, two widely used search methods based on sequence-profile and profile-profile comparison. Due to their closeness to actual protein sequences, clade-centered models are shown to be more specific and functionally predictive than the broadly used consensus models. Based on them, we improved annotation of Plasmodium falciparum protein sequences on a scale not previously possible. We successfully predict at least one domain for 72% of P. falciparum proteins against 63% achieved previously, corresponding to 30% of improvement over the total number of Pfam domain predictions on the whole genome. The method is applicable to any genome and opens new avenues to tackle evolutionary questions such as the reconstruction of ancient domain duplications, the reconstruction of the history of protein architectures, and the estimation of protein domain age. Website and software: http://www.lcqb.upmc.fr/CLADE.
Current sequence databases contain hundreds of billions of nucleotides coding for genes and a classification of these sequences is a primary problem in genomics. A reasonable way to organize these sequences is through their predicted domains, but the identification of domains in very divergent sequences, spanning the entire phylogenetic tree of species, is a difficult problem. By generating multiple probabilistic models for a domain, describing the spread of evolutionary patterns in different phylogenetic clades, we can effectively explore domains that are likely to be coded in gene sequences. Through a machine learning approach and optimization techniques, coding for expected evolutionary constraints, we filter the many possibilities of domain identification found for a gene and propose the most likely domain architecture associated to it. The application of this novel approach to the full genome of Plasmodium falciparum, to a dataset of sequences from three SCOP datasets highlights the interest of exploring multiple pathways of domain evolution in the aim of extracting biological information from genomic sequences. Our new computational approach was developed with the hope of providing a novel tier of accurate and precise tools that complement existing tools such as HMMer, HHblits and PSI-BLAST, by exploring in a novel way the large amount of sequence data available. The existence of powerful databases for sequences, domains and architectures help make this hope a reality.
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