title: Sma3s: a three-step modular annotator for large sequence datasets.
abstract: Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ~85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes.
authors: Integrated Bioinformatics, National Institute for Bioinformatics, University of Málaga, Campus de Teatinos, Spain.
authors: Antonio
authors: A
authors: Muñoz-Mérida
authors: Cellular Biology, Genetics and Physiology Department, University of Málaga, Campus de Teatinos, Spain.
authors: Enrique
authors: E
authors: Viguera
authors: Molecular Biology and Biochemistry Department, University of Málaga, Campus de Teatinos, Spain.
authors: M Gonzalo
authors: MG
authors: Claros
authors: Integrated Bioinformatics, National Institute for Bioinformatics, University of Málaga, Campus de Teatinos, Spain Computer Architecture Department, University of Málaga, Campus de Teatinos, Spain.
authors: Oswaldo
authors: O
authors: Trelles
authors: Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC-JA), Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, Sevilla 41013, Spain ajperez@upo.es.
authors: Antonio J
authors: AJ
authors: Pérez-Pulido
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D058977:Molecular Sequence Annotation; D012984:Software
keywords: bioinformatic tool; functional annotation; genome annotation; transcriptome annotation