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BMCBI
2008
86views more  BMCBI 2008»
13 years 4 months ago
Predicting protein linkages in bacteria: Which method is best depends on task
Background: Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting link...
Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill,...
BMCBI
2005
152views more  BMCBI 2005»
13 years 4 months ago
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Background: Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling ar...
Markus Wistrand, Erik L. L. Sonnhammer
SNPD
2004
13 years 6 months ago
Using extended phylogenetc profiles and support vector machines for protein family classification
We proposed a new approach to compare profiles when the correlations among attributes can be represented as a tree. To account for these correlations, the profile is extended with...
Kishore Narra, Li Liao
BMCBI
2011
12 years 11 months ago
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
Background: Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diver...
Ozkan U. Nalbantoglu, Samuel F. Way, Steven H. Hin...
BMCBI
2007
144views more  BMCBI 2007»
13 years 4 months ago
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic ge
Background: Although many genomic features have been used in the prediction of proteinprotein interactions (PPIs), frequently only one is used in a computational method. After rea...
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan ...