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» MISAE: A New Approach for Regulatory Motif Extraction
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BMCBI
2006
136views more  BMCBI 2006»
13 years 6 months ago
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
Background: Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DN...
Jianjun Hu, Yifeng D. Yang, Daisuke Kihara
BMCBI
2008
78views more  BMCBI 2008»
13 years 6 months ago
A new protein linear motif benchmark for multiple sequence alignment software
Background: Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational ...
Emmanuel Perrodou, Claudia Chica, Olivier Poch, To...
WABI
2009
Springer
14 years 1 months ago
MADMX: A Novel Strategy for Maximal Dense Motif Extraction
We develop, analyze and experiment with a new tool, called madmx, which extracts frequent motifs, possibly including don’t care characters, from biological sequences. We introduc...
Roberto Grossi, Andrea Pietracaprina, Nadia Pisant...
BMCBI
2011
12 years 10 months ago
RAG: An Update to the RNA-As-Graphs Resource
Background: In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structur...
Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tam...
BMCBI
2006
120views more  BMCBI 2006»
13 years 6 months ago
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse
Background: Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. ...
Ryung S. Kim, Hongkai Ji, Wing Hung Wong