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Materias / palabras clave: Catálogos automatizados; Catálogos de bibliotecas; Datos; Datos bibliográficos; Computadoras; Data mining; Catalogs, Classified; Cataloging; Data processing; Online bibliographic searching; Opac

MOTIVATION: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. RESULTS: UBLAST and USEARCH are new algorithms enabling sensitive ...

SUMMARY: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one app...

A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of ...

Materias / palabras clave: Bottleneck; Metagenomics; Computer science; Diamond; Sensitivity (control systems); Software; Search engine indexing; Speedup; Computational biology; Data mining; Bioinformatics; Parallel computing

The program Mercury , developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module...

BACKGROUND: Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST s...

MOTIVATION: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently clust...

MOTIVATION: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has be...

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the origi...

BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to...

A new method for automatic indexing and retrieval is described. The approach is to take advantage of implicit higher-order structure in the association of terms with documents (“semantic structure”) in order to impro...

MOTIVATION: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated ...

We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence...

BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacr...

Materias / palabras clave: data search and mining, big data integrity and privacy, artificial intelligence, cognitive modeling, data storage, robots and control systems; Technology