Articles
Volume 6 (2005) - April 2005
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Methodology article
Irina Abnizova, Rene te Boekhorst, Klaudia Walter, Walter R Gilks BMC Bioinformatics 2005, 6:109 (27 April 2005) |
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Research article
Erik LL Sonnhammer, Volker Hollich BMC Bioinformatics 2005, 6:108 (27 April 2005) |
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Methodology article
Scott L Carter, Aron C Eklund, Brigham H Mecham, Isaac S Kohane, Zoltan Szallasi BMC Bioinformatics 2005, 6:107 (25 April 2005) |
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Methodology article
Hua Liu, Sergey Tarima, Aaron S Borders, Thomas V Getchell, Marilyn L Getchell, Arnold J Stromberg BMC Bioinformatics 2005, 6:106 (25 April 2005) |
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Research article
Detailed protein sequence alignment based on Spectral Similarity Score (SSS) Kshitiz Gupta, Dina Thomas, SV Vidya, KV Venkatesh, S Ramakumar BMC Bioinformatics 2005, 6:105 (23 April 2005) Inspired by music database retrieval systems, this algorithm establishes spectral similarity between two amino acid sequences based on 256 attributes, detecting local variations and sub-sequence similarities that character-based algorithms miss.
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Research article
Nikolaos G Sgourakis, Pantelis G Bagos, Panagiotis K Papasaikas, Stavros J Hamodrakas BMC Bioinformatics 2005, 6:104 (22 April 2005) |
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Methodology article
AM Cohen, WR Hersh, C Dubay, K Spackman BMC Bioinformatics 2005, 6:103 (22 April 2005) |
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Research article
Evolutionary distance estimation and fidelity of pair wise sequence alignment Michael S Rosenberg BMC Bioinformatics 2005, 6:102 (19 April 2005) |
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Software
MARS: Microarray analysis, retrieval, and storage system Michael Maurer, Robert Molidor, Alexander Sturn, Juergen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler, Zlatko Trajanoski BMC Bioinformatics 2005, 6:101 (18 April 2005) The MARS suite for microarray data is fully MIAME compliant, and provides a lab notebook and laboratory information management system, integrated with a pipeline of image analysis, normalization, gene expression clustering and pathway mapping.
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Research article
Filtering high-throughput protein-protein interaction data using a combination of genomic features Ashwini Patil, Haruki Nakamura BMC Bioinformatics 2005, 6:100 (18 April 2005) Gene ontology annotations, sequence alignment and structural information of Pfam domains have been combined to create a method of validating high-thoroughput protein-protein interaction data that functions with a sensitivity of 90% and specificity of 63%.
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Research article
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER Markus Wistrand, Erik LL Sonnhammer BMC Bioinformatics 2005, 6:99 (15 April 2005) |
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Software
ProGenExpress: Visualization of quantitative data on prokaryotic genomes Michael Watson BMC Bioinformatics 2005, 6:98 (13 April 2005) |
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Research article
Leslie R Grate BMC Bioinformatics 2005, 6:97 (13 April 2005) |
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Software
PREP-Mt: predictive RNA editor for plant mitochondrial genes Jeffrey P Mower BMC Bioinformatics 2005, 6:96 (12 April 2005) |
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Software
Judith E Stenger, Hong Xu, Carol Haynes, Elizabeth R Hauser, Margaret Pericak-Vance, Pascal J Goldschmidt-Clermont, Jeffery M Vance BMC Bioinformatics 2005, 6:95 (12 April 2005) |
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Software
'PACLIMS': A component LIM system for high-throughput functional genomic analysis Nicole Donofrio, Ravi Rajagopalon, Douglas Brown, Stephen Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas Mitchell, Natalia Galadima, Sara Tucker, Marc J Orbach, Gayatri Patel, Mark Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee, Ralph A Dean BMC Bioinformatics 2005, 6:94 (12 April 2005) |
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Software
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST) Scot E Dowd, Joaquin Zaragoza, Javier R Rodriguez, Melvin J Oliver, Paxton R Payton BMC Bioinformatics 2005, 6:93 (8 April 2005) W.ND-BLAST allows an increase in the performance of BLAST by distributing queries across a local area network, providing an intuitive GUI for database creation, search execution, output evaluation, and result exportation.
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Research article
Shortest triplet clustering: reconstructing large phylogenies using representative sets Le Sy Vinh, Arndt von Haeseler BMC Bioinformatics 2005, 6:92 (8 April 2005) |
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Software
Andreas Möglich, Daniel Weinfurtner, Till Maurer, Wolfram Gronwald, Hans Kalbitzer BMC Bioinformatics 2005, 6:91 (8 April 2005) |
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Methodology article
Mark J Gibbs, John S Armstrong, Adrian J Gibbs BMC Bioinformatics 2005, 6:90 (8 April 2005) |
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Methodology article
A method for aligning RNA secondary structures and its application to RNA motif detection Jianghui Liu, Jason TL Wang, Jun Hu, Bin Tian BMC Bioinformatics 2005, 6:89 (7 April 2005) RSmatch aligns structures and identifies functional motifs by decomposing RNA secondary structures into sets of atomic structure components, finding the optimal global and local alignments using two scoring matrices.
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Methodology article
Building a protein name dictionary from full text: a machine learning term extraction approach Lei Shi, Fabien Campagne BMC Bioinformatics 2005, 6:88 (7 April 2005) A data mining approach, collecting high frequency terms in full text and using machine learning to identify biological terms, is used to construct a protein name dictionary which recognises many name variants not found in SwissProt.
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Methodology article
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator Alexander Garcia Castro, Samuel Thoraval, Leyla J Garcia, Mark A Ragan BMC Bioinformatics 2005, 6:87 (7 April 2005) |
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Software
Prinal Trivedi, Jode W Edwards, Jelai Wang, Gary L Gadbury, Vinodh Srinivasasainagendra, Stanislav O Zakharkin, Kyoungmi Kim, Tapan Mehta, Jacob PL Brand, Amit Patki, Grier P Page, David B Allison BMC Bioinformatics 2005, 6:86 (6 April 2005) |
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Software
CGHPRO – A comprehensive data analysis tool for array CGH Wei Chen, Fikret Erdogan, H-Hilger Ropers, Steffen Lenzner, Reinhard Ullmann BMC Bioinformatics 2005, 6:85 (5 April 2005) |
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Research article
Scoring functions for transcription factor binding site prediction Markus Friberg, Peter von Rohr, Gaston Gonnet BMC Bioinformatics 2005, 6:84 (4 April 2005) |
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Methodology article
Bayesian coestimation of phylogeny and sequence alignment Gerton Lunter, István Miklós, Alexei Drummond, Jens Jensen, Jotun Hein BMC Bioinformatics 2005, 6:83 (1 April 2005) A fully Bayesian Markov chain Monte Carlo method combines multiple sequence alignment and phylogeny, while taking full account of their inter-dependence and reveals new biologically meaningful information that is not available through standard methods
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Methodology article
Super paramagnetic clustering of protein sequences Igor V Tetko, Axel Facius, Andreas Ruepp, Hans-Werner Mewes BMC Bioinformatics 2005, 6:82 (1 April 2005) |
