Bioinformatics

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Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
Bioinformatics - Tập 21 Số 13 - Trang 3001-3008 - 2005
Jiang Gui, Hongzhe Li
UCHIME improves sensitivity and speed of chimera detection
Bioinformatics - Tập 27 Số 16 - Trang 2194-2200 - 2011
Robert C. Edgar, Brian J. Haas, José C. Clemente, Christopher Quince, Rob Knight
Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between population... hiện toàn bộ
Optimal alignments in linear space
Bioinformatics - Tập 4 Số 1 - Trang 11-17 - 1988
Eugene W. Myers, Webb Miller
InterProScan 5: genome-scale protein function classification
Bioinformatics - Tập 30 Số 9 - Trang 1236-1240 - 2014
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka, Sebastien Pesseat, A. F. Quinn, Amaia Sangrador‐Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo López, Sarah Hunter
Abstract Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and t... hiện toàn bộ
BEDTools: a flexible suite of utilities for comparing genomic features
Bioinformatics - Tập 26 Số 6 - Trang 841-842 - 2010
Aaron R. Quinlan, Ira M. Hall
Abstract 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 by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these ... hiện toàn bộ
Two-stage designs for experiments with a large number of hypotheses
Bioinformatics - Tập 21 Số 19 - Trang 3771-3777 - 2005
Sonja Zehetmayer, Péter Bauer, Martin Posch
QuickGO: a web-based tool for Gene Ontology searching
Bioinformatics - Tập 25 Số 22 - Trang 3045-3046 - 2009
David Binns, Emily Dimmer, Rachael P. Huntley, Daniel Barrell, Claire O’Donovan, Rolf Apweiler
Abstract Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can ... hiện toàn bộ
The role of indirect connections in gene networks in predicting function
Bioinformatics - Tập 27 Số 13 - Trang 1860-1866 - 2011
Jesse Gillis, Paul Pavlidis
AbstractMotivation: Gene networks have been used widely in gene function prediction algorithms, many based on complex extensions of the ‘guilt by association’ principle. We sought to provide a unified explanation for the performance of gene function prediction algorithms in exploiting network structure and thereby simplify future analysis.Results: We use co-expression networks to show that most ex... hiện toàn bộ
ProtTest 3: fast selection of best-fit models of protein evolution
Bioinformatics - Tập 27 Số 8 - Trang 1164-1165 - 2011
Diego Darriba, Guillermo L. Taboada, Ramón Doallo, David Posada
Abstract Summary: We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities. Availability: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked... hiện toàn bộ
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
Bioinformatics - Tập 26 Số 19 - Trang 2455-2457 - 2010
Wayne Delport, Art F. Y. Poon, Simon D. W. Frost, Sergei L. Kosakovsky Pond
Abstract Summary: Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapid... hiện toàn bộ
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