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» Analysis of computational approaches for motif discovery
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BCBGC
2008
14 years 11 months ago
BMA - Boolean Matrices as Model for Motif Kernels
We introduce the data model BM, which specifies kernels of motifs by means of Boolean matrices. Different from position frequency matrices these only specify which bases can appea...
Jan Schröder, Manfred Schimmler, Heiko Schr&o...
RECOMB
2004
Springer
15 years 9 months ago
Multiple organism gene finding by collapsed gibbs sampling
The Gibbs sampling method has been widely used for sequence analysis after it was successfully applied to the problem of identifying regulatory motif sequences upstream of genes. ...
Sourav Chatterji, Lior Pachter
IMSCCS
2006
IEEE
15 years 3 months ago
Frequency Distribution of TATA Box and Extension Sequences on Human Promoters
Background: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. Results: In this study, we cond...
Wei Shi, Wanlei Zhou
CSB
2003
IEEE
15 years 2 months ago
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences
The promise of plentiful data on common human genetic variations has given hope that we will be able to uncover genetic factors behind common diseases that have proven difficult ...
Russell Schwartz
SAC
2004
ACM
15 years 2 months ago
A parallel algorithm for the extraction of structured motifs
In this work we propose a parallel algorithm for the efficient extraction of binding-site consensus from genomic sequences. This algorithm, based on an existing approach, extracts...
Alexandra M. Carvalho, Arlindo L. Oliveira, Ana T....