Benchmarking tools for the alignment of functional noncoding DNA
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* Corresponding author: Casey M Bergman cbergman@gen.cam.ac.uk
BMC Bioinformatics 2004, 5:6 doi:10.1186/1471-2105-5-6
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Cgaln: fast and space-efficient whole-genome alignment Ryuichiro Nakato, Osamu Gotoh BMC Bioinformatics 2010, 11:224 (30 April 2010) |
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Towards realistic benchmarks for multiple alignments of non-coding sequences Jaebum Kim, Saurabh Sinha BMC Bioinformatics 2010, 11:54 (26 January 2010) |
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Software
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Avinash Varadarajan, Robert K Bradley, Ian H Holmes Genome Biology 2008, 9:R147 (8 October 2008) Three tools for simulating genome evolution are presented: for neutrally evolving DNA, for phylogenetic context-free grammars and for richly structured syntenic blocks of genome sequence. |
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Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida BMC Bioinformatics 2008, 9:112 (22 February 2008) |
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Rekin's Janky, Jacques van Helden BMC Bioinformatics 2008, 9:37 (23 January 2008) |
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Research article
How accurately is ncRNA aligned within whole-genome multiple alignments? Adrienne X Wang, Walter L Ruzzo, Martin Tompa BMC Bioinformatics 2007, 8:417 (26 October 2007) |
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Research
Weichun Huang, Joseph R Nevins, Uwe Ohler Genome Biology 2007, 8:R225 (24 October 2007) Phylogenetic simulation of promoter evolution were used to analyze functional site turnover in regulatory sequences. |
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Research
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon Genome Biology 2007, 8:R101 (5 June 2007) Analysis of 280 experimentally-verified |
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Research article
Considerations in the identification of functional RNA structural elements in genomic alignments Tomas Babak, Benjamin J Blencowe, Timothy R Hughes BMC Bioinformatics 2007, 8:33 (30 January 2007) Search tools perform poorly at finding noncoding RNAs on a test set of known ncRNAs for which the sequences are randomly shuffled, although a combination of conservation and thermodynamic stability has promise for ncRNA detection.
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Software
Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi BMC Bioinformatics 2006, 7:472 (24 October 2006) |
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Research article
Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen BMC Bioinformatics 2006, 7:376 (14 August 2006) |
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Methodology article
Jun Wang, Peter D Keightley, Toby Johnson BMC Bioinformatics 2006, 7:292 (8 June 2006) |
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Research
Multiple sequence alignment with user-defined anchor points Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler, Peter F Stadler Algorithms for Molecular Biology 2006, 1:6 (19 April 2006) |
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Software
Arthur Shih, DT Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, Mu-Fen Hsieh BMC Bioinformatics 2006, 7:103 (2 March 2006) |
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Research article
Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata BMC Bioinformatics 2005, 6(Suppl 4):S22 (1 December 2005) |
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Research article
Multiple sequence alignment accuracy and evolutionary distance estimation Michael S Rosenberg BMC Bioinformatics 2005, 6:278 (23 November 2005) |
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Software
Genomic multiple sequence alignments: refinement using a genetic algorithm Chunlin Wang, Elliot J Lefkowitz BMC Bioinformatics 2005, 6:200 (8 August 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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Research article
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran R Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern BMC Bioinformatics 2005, 6:66 (22 March 2005) |
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Method
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004) MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments. |
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Software
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern BMC Bioinformatics 2004, 5:128 (9 September 2004) |
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Research
Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker Genome Biology 2004, 5:R61 (20 August 2004) 27 predicted gene-regulatory regions in the |
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Correction
Correction: Benchmarking tools for the alignment of functional noncoding DNA DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen BMC Bioinformatics 2004, 5:73 (8 June 2004) |