MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
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* Corresponding author: Jun Wang j.wang-13@sms.ed.ac.uk
BMC Bioinformatics 2006, 7:292 doi:10.1186/1471-2105-7-292
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BioMed Central: 4 citations
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Research article
Patterns of selective constraints in noncoding DNA of rice Xingyi Guo, Yu Wang, Peter D Keightley, Longjiang Fan BMC Evolutionary Biology 2007, 7:208 (1 November 2007) |
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Research article
Leah J DeRose-Wilson, Brandon S Gaut BMC Evolutionary Biology 2007, 7:66 (23 April 2007) Nucleotide substitution rate variation in the intergenic regions of Arabidopsis thaliana relative to A. lyrata is linked to GC content and gene density, suggesting that the apparent selective constraint may be illusory, an effect of base composition.
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Research
Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over Penelope R Haddrill, Daniel L Halligan, Dimitris Tomaras, Brian Charlesworth Genome Biology 2007, 8:R18 (6 February 2007) Observations from a genome-wide comparison of |
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Methodology article
Logarithmic gap costs decrease alignment accuracy Reed A Cartwright BMC Bioinformatics 2006, 7:527 (5 December 2006) Because the distribution of indel sizes follows a power law, using logarithmic gap costs was expected to give biologically authentic sequence alignments, but this actually lowers accuracy compared to existing algorithms that use affine gap costs.
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