Miguel Reboiro-Jato

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ALTER is an open web-based tool to transform between different multiple sequence alignment formats. The originality of ALTER lies in the fact that it focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. In addition, ALTER is capable of identify and remove identical(More)
Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allow for efficient generation, deployment and reutilization of such biomedical(More)
Nowadays, document classification has become an interesting research field. Partly, this is due to the increasing availability of biomedical information in digital form which is necessary to catalogue and organize. In this context, machine learning techniques are usually applied to text classification by using a general inductive process that automatically(More)
S-RNase-based gametophytic self-incompatibility evolved once before the split of the Asteridae and Rosidae. In Prunus (tribe Amygdaloideae of Rosaceae), the self-incompatibility S-pollen is a single F-box gene that presents the expected evolutionary signatures. In Malus and Pyrus (subtribe Pyrinae of Rosaceae), however, clusters of F-box genes (called(More)
Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the(More)
Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being(More)
Next-generation sequencing (NGS) technologies are making sequence data available on an unprecedented scale. In this context, new catalogs of Single Nucleotide Polymorphism and mutations generated by resequencing studies are usually stored in genome position files (e.g. Variant Call Format, SAMTools pileup, BED, GFF) comprising of large lists of genomic(More)
Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models.(More)
BACKGROUND Genomic position (GP) files currently used in next-generation sequencing (NGS) studies are always difficult to manipulate due to their huge size and the lack of appropriate tools to properly manage them. The structure of these flat files is based on representing one line per position that has been covered by at least one aligned read, imposing(More)