HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences

scientific article

HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/bmcbi/SrivastavaDNL07
P356DOI10.1186/1471-2105-8-104
P932PMC publication ID1852395
P698PubMed publication ID17389042
P5875ResearchGate publication ID6418546

P50authorDhwani K DesaiQ42415673
P2093author name stringPrashant K Srivastava
Andrew M Lynn
Soumyadeep Nandi
P2860cites workHybrid alignment: high-performance with universal statistics.Q52038190
Analysis and prediction of functional sub-types from protein sequence alignments.Q52072935
A learning method of hidden Markov models for sequence discrimination.Q52203520
A discriminative framework for detecting remote protein homologiesQ62494112
Functional classification using phylogenomic inferenceQ21145680
A comprehensive update of the sequence and structure classification of kinasesQ21256426
The ENZYME database in 2000Q22242849
Gene ontology: tool for the unification of biologyQ23781406
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
The Pfam protein families databaseQ24599089
MUSCLE: multiple sequence alignment with high accuracy and high throughputQ24613456
Improved tools for biological sequence comparisonQ24652199
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMERQ24801213
Basic local alignment search toolQ25938991
ALSCRIPT: a tool to format multiple sequence alignmentsQ27860540
SCOP: a structural classification of proteins database for the investigation of sequences and structuresQ27860689
The conformational plasticity of protein kinasesQ27860946
Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classificationQ28131753
The relationship between protein structure and function: a comprehensive survey with application to the yeast genomeQ28144049
Protein homology detection by HMM-HMM comparisonQ28292161
Classifying G-protein coupled receptors with support vector machinesQ28679184
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrapQ29544639
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structureQ29547343
Assessing the accuracy of prediction algorithms for classification: an overviewQ29615358
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinasesQ34957027
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenaseQ37204360
Improving profile HMM discrimination by adapting transition probabilitiesQ44852949
Subfamily hmms in functional genomics.Q45945006
COACH: profile-profile alignment of protein families using hidden Markov modelsQ47611123
Structural and functional aspects of G protein-coupled receptor oligomerizationQ47835591
P304page(s)104
P577publication date2007-03-27
P1433published inBMC BioinformaticsQ4835939
P1476titleHMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences
P478volume8

Reverse relations

cites work (P2860)
Q37319684Augmented training of hidden Markov models to recognize remote homologs via simulated evolution
Q46336917Configurational assignment of secondary hydroxyl groups and methyl branches in polyketide natural products through bioinformatic analysis of the ketoreductase domain
Q28474339Employing information theoretic measures and mutagenesis to identify residues critical for drug-proton antiport function in Mdr1p of Candida albicans
Q42415610Factors influencing the diversity of iron uptake systems in aquatic microorganisms
Q30524686Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum
Q64055375Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723
Q35215270HMM-ModE: implementation, benchmarking and validation with HMMER3.
Q37700192Hidden Markov Models and their Applications in Biological Sequence Analysis
Q51724542Identification of putative Z-ring-associated proteins, involved in cell division in human pathogenic bacteria Helicobacter pylori.
Q42599526ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities
Q28472226Rational mutational analysis of a multidrug MFS transporter CaMdr1p of Candida albicans by employing a membrane environment based computational approach