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» Comparative modeling without implicit sequence alignments
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BMCBI
2006
86views more  BMCBI 2006»
13 years 8 months ago
MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
Background: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unravel...
Jun Wang, Peter D. Keightley, Toby Johnson
BMCBI
2008
128views more  BMCBI 2008»
13 years 8 months ago
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor bindin
Background: Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (T...
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mari...
RECOMB
1997
Springer
14 years 21 days ago
Sequence alignment with tandem duplication
Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modi cation of sequen...
Gary Benson
BMEI
2008
IEEE
14 years 3 months ago
A New Approach for Tree Alignment Based on Local Re-Optimization
Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences align...
Feng Yue, Jijun Tang
RECOMB
2003
Springer
14 years 8 months ago
Accurate detection of very sparse sequence motifs
Protein sequence alignments are more reliable the shorter the evolutionary distance. Here, we align distantly related proteins using many closely spaced intermediate sequences as ...
Andreas Heger, Michael Lappe, Liisa Holm