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» Overestimation for Multiple Sequence Alignment
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BMCBI
2005
169views more  BMCBI 2005»
13 years 7 months ago
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
JDA
2008
87views more  JDA 2008»
13 years 7 months ago
Lossless filter for multiple repetitions with Hamming distance
Similarity search in texts, notably in biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been create...
Pierre Peterlongo, Nadia Pisanti, Fréd&eacu...
RECOMB
2004
Springer
14 years 8 months ago
Designing multiple simultaneous seeds for DNA similarity search
The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of...
Yanni Sun, Jeremy Buhler
BMCBI
2010
177views more  BMCBI 2010»
13 years 7 months ago
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets
Background: Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize mu...
Aydin Albayrak, Hasan H. Otu, Ugur O. Sezerman
BMCBI
2005
100views more  BMCBI 2005»
13 years 7 months ago
Scoredist: A simple and robust protein sequence distance estimator
Background: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from ...
Erik L. L. Sonnhammer, Volker Hollich