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» Automatic Structures: Richness and Limitations
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BMCBI
2008
145views more  BMCBI 2008»
13 years 4 months ago
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Background: Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are ...
Jonathan R. Manning, Emily R. Jefferson, Geoffrey ...
BMCBI
2007
116views more  BMCBI 2007»
13 years 4 months ago
primetv: a viewer for reconciled trees
Background: Evolutionary processes, such as gene family evolution or parasite-host cospeciation, can often be viewed as a tree evolving inside another tree. Relating two given tre...
Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglun...
BMCBI
2008
149views more  BMCBI 2008»
13 years 4 months ago
Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment s
Background: Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic d...
Olivier Bastien, Eric Maréchal
BMCBI
2006
116views more  BMCBI 2006»
13 years 4 months ago
Optimized mixed Markov models for motif identification
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
PR
2008
141views more  PR 2008»
13 years 4 months ago
Robust and efficient multiclass SVM models for phrase pattern recognition
Phrase pattern recognition (phrase chunking) refers to automatic approaches for identifying predefined phrase structures in a stream of text. Support vector machines (SVMs)-based ...
Yu-Chieh Wu, Yue-Shi Lee, Jie-Chi Yang