Tag Archives: alignment

The GPU hype and bioinformatics algorithms

I am a big fan of GPU computing (and other “alternative” hardware), but it was refreshing to read this commentary by Lars Jensen, which I could summarize by this statement: You do not see anyone publishing papers with titles like … Continue reading

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fault-tolerant conversion between sequence alignments

Despite I’m very charitable when testing my own programs, I’m not so nice when asked to scrutinize other people’s work. That’s why I was happy to see the announcement about the ALTER web server being published at Nucleic Acids Research … Continue reading

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Using System-on-a-Chip hardware to speed up alignments

In recent years there has been an explosion of parallel algorithms for solving bioinformatics problems, namely phylogenetic reconstruction and sequence alignment. These algorithms follow the growth of new hardware solutions like  Field-Programmable Gate Arrays (integrated circuits capable of  performing simple … Continue reading

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arxiv – recent articles on phylogenetics

obs: manuscripts deposited on the arxiv repository may have not been peer reviewed. An alternative marginal likelihood estimator for phylogenetic models. (arXiv:1001.2136v1 [stat.CO]) by Serena Arima, Luca Tardella Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular … Continue reading

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Molecular Biology and Evolution 2010 Volume 27, Number 2

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, by Gouy, M., Guindon, S., Gascuel, O. Molecular Biology and Evolution 2010 27(2):221-224; doi:10.1093/molbev/msp259 We present SeaView version 4, a multiplatform program designed to facilitate … Continue reading

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Bioinformatics – Volume 26, Number 2, 15 January 2010

Target prediction and a statistical sampling algorithm for RNA-RNA interaction — Huang, F. W. D., Qin, J., Reidys, C. M., Stadler, P. F. 26 (2): 175 — Bioinformatics: Motivation: It has been proven that the accessibility of the target sites … Continue reading

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