HHsenser: exhaustive transitive profile search using HMM–HMM comparison
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Summary
HHsenser is the first server to offer exhaustive intermediate profile searches, which it combines with pairwise comparison of hidden Markov models to make it a useful tool for evolutionary studies and aid applications that rely on diverse multiple sequence alignments as input.
- Type
- article
- Published
- 2006-07-01
- Cited by
- 85
- References
- 31
- Access
- Open access
- OpenAlex
- https://openalex.org/W1998445752
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9807376
Keywords
Hidden Markov model, Biology, Multiple sequence alignment, Pairwise comparison, False positive paradox
References
- PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
- The P5 protein from bacteriophage phi‐6 is a distant homolog of lytic transglycosylases
- Fold recognition without folds
- AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.
- HHrep: de novo protein repeat detection and the origin of TIM barrels
- Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information
- Alignments grow, secondary structure prediction improves
- Intermediate sequences increase the detection of homology between sequences.
- The HHpred interactive server for protein homology detection and structure prediction
- Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
- Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
- Hidden Markov models in computational biology. Applications to protein modeling.
- In silico identification of functional regions in proteins
- Sequence clustering strategies improve remote homology recognitions while reducing search times.
- Better prediction of sub‐cellular localization by combining evolutionary and structural information
- Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
- Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
- An evolutionary trace method defines binding surfaces common to protein families.
- CLANS: a Java application for visualizing protein families based on pairwise similarity
- Analysis and prediction of functional sub-types from protein sequence alignments.
Cited by
- Method for recognizing local descriptors of protein structures using Hidden Markov Models
- Toward a molecular understanding of yeast silent chromatin : roles for H4K16 acetylation and the Sir3 C-terminus
- Estudos evolutivos do divisomo, um complexo multiprotéico responsável pela divisão bacteriana
- Essential role of the disintegrin-like domain in ADAMTS13 function.
- Inhibition of Mycobacterium tuberculosis PknG by non-catalytic rubredoxin domain specific modification: reaction of an electrophilic nitro-fatty acid with the Fe–S center
- Decreased transcriptional activity of calcium-sensing receptor gene promoter 1 is associated with calcium nephrolithiasis.
- Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor.
- Discrete - Continuous Duality of Protein Structure Space
- Bioinformatics Analysis Identify Novel OB Fold Protein Coding Genes in C. elegans
- Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica
- COMPASS server for remote homology inference
- Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1
- Protein Domain of Unknown Function 3233 is a Translocation Domain of Autotransporter Secretory Mechanism in Gamma proteobacteria
- The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold
- Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction.
- Needle in the haystack: structure-based toxin discovery.
- HHomp—prediction and classification of outer membrane proteins
- Bioinformatics of the TULIP domain superfamily.
- Fold and Function of the InlB B-repeat*
- Dimerization of Sir3 via its C‐terminal winged helix domain is essential for yeast heterochromatin formation
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