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» Suboptimal Alignments Improve the Detection of Weak Homologs...
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BIBE
2005
IEEE
126views Bioinformatics» more  BIBE 2005»
9 years 8 months ago
Suboptimal Alignments Improve the Detection of Weak Homologs in Sequence Database Searches
PSI-BLAST remains one of the popular tools for searching remote homologs in sequence databases. We recently demonstrated that hybrid alignment can function as the alignment core f...
Yuheng Li, Mario Lauria, Ralf Bundschuh
BMCBI
2010
101views more  BMCBI 2010»
9 years 2 months ago
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment
Background: Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stri...
Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst,...
BMCBI
2010
137views more  BMCBI 2010»
9 years 2 months ago
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
Background: While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor ...
Michael L. Sierk, Michael E. Smoot, Ellen J. Bass,...
JCB
2002
116views more  JCB 2002»
9 years 1 months ago
A Novel Approach to Remote Homology Detection: Jumping Alignments
We describe a new algorithm for protein classi cation and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alig...
Rainer Spang, Marc Rehmsmeier, Jens Stoye
BMCBI
2007
142views more  BMCBI 2007»
9 years 2 months ago
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addre...
Juliana S. Bernardes, Alberto M. R. Dávila,...
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