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60
Protein homology detection by HMM-HMM comparison
- BIOINFORMATICS
, 2005
"... Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile H ..."
Abstract
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Cited by 401 (8 self)
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HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach. The method (HHsearch) is benchmarked together with BLAST, PSI-BLAST, HMMER, and the profile-profile comparison tools PROF_SIM and COMPASS, in an all-against-all compari-son of a database
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
- J. Mol. Biol
, 2003
"... We present a novel method for the comparison of multiple protein align-ments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile–profile alignments and analytically estimates E-values for the detected similari ..."
Abstract
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Cited by 125 (33 self)
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similarities. The scoring system and E-value calculation are based on a generalization of the PSI-BLAST approach to profile–sequence comparison, which is adapted for the profile–profile case. Tested along with existing methods for profile–sequence (PSI-BLAST) and profile– profile (prof_sim) comparison, COMPASS
localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
, 2004
"... Automated prediction of subcellular localization of proteins is an important step in the functional annotation of genomes. The existing subcellular localization prediction methods are based on either amino acid composition or N-terminal characteristics of the proteins. In this paper, support vector ..."
Abstract
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features of a protein, which consisted of an input vector of 458 dimensions (400 dipeptide compositions, 33 properties, 20 amino acid compositions of the protein and 5 from PSI-BLAST output). Using this hybrid approach, the prediction accuraciesofnuclear,cytoplasmic,mitochondrialand extracellular proteins
PSIBLAST PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance
- Bioinformatics
"... Summary: We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using pairwise statistical significance. Using position-specific substitution matrices to estimate pairwise statistical significance has been recently shown to give promising results in terms of retrieval accuracy, w ..."
Abstract
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Cited by 6 (2 self)
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, which motivates its use to refine PSI-BLAST results, since PSI-BLAST also constructs a position-specific substitution matrix for the query sequence during the search. The obvious advantage of the approach is more accurate estimates of statistical significance because of pairwise statistical significance
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
- Nucleic Acids Research
, 2004
"... Automated prediction of subcellular localization of proteins is an important step in the functional annota-tion of genomes. The existing subcellular localization prediction methods are based on either amino acid composition or N-terminal characteristics of the pro-teins. In thispaper, support vector ..."
Abstract
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Cited by 62 (6 self)
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of a protein, which consisted of an input vector of 458 dimensions (400 dipeptide compositions, 33 properties, 20 amino acid compositions of the protein and 5 from PSI-BLAST output). Using this hybrid approach, the prediction accuraciesofnuclear,cytoplasmic,mitochondrialand extracellular proteins
Sequence analysis Simple is beautiful: a straightforward approach to improve the de- lineation of true and false positives in PSI-BLAST searches
"... Motivation: The deluge of biological information from different ge-nomic initiatives and the rapid advancement in biotechnologies have made bioinformatics tools an integral part of modern biology. Among the widely-used sequence alignment tools, BLAST and PSI-BLAST are arguably the most popular. PSI- ..."
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. Nevertheless, corruption of its profile via the incorporation of false positive sequences remains a major chal-lenge. Results: We have developed a simple and elegant approach to resolve the problem of model corruption in PSI-BLAST searches. We hypothesized that combining results from the first (least
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
, 2006
"... Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently ..."
Abstract
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Cited by 6 (4 self)
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. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is 35 % better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and Swiss
Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage
- PloS ONE
, 2013
"... Background: Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectivel ..."
Abstract
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Cited by 5 (3 self)
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homologues which could not be obtained using PSI-BLAST. Methodology/Principal Findings: We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based
Nucleic Acids Research Advance Access published March 16, 2007 Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments
, 2006
"... Sequence alignments may be the most fundamental computational resource for molecular biology. The best methods that identify sequence relatedness through profile–profile comparisons are much slower and more complex than sequence–sequence and sequence–profile comparisons such as, respectively, BLAST ..."
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and PSI-BLAST. Families of related genes and gene products (proteins) can be represented by consensus sequences that list the nucleic/amino acid most frequent at each sequence position in that family. Here, we propose a novel approach for consensus-sequence-based comparisons. This approach improved
Within the Twilight Zone: A Sensitive Profile-Profile Comparison Tool Based on Information Theory
- J. Mol. Biol
, 2002
"... This paper presents a novel approach to prole-prole comparison. The method compares two input proles (like those that are generated by PSI-BLAST) and assigns a similarity score to assess their statistical similarity. Our prole-prole comparison tool, which allows for gaps, can be used to detect weak ..."
Abstract
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Cited by 147 (4 self)
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This paper presents a novel approach to prole-prole comparison. The method compares two input proles (like those that are generated by PSI-BLAST) and assigns a similarity score to assess their statistical similarity. Our prole-prole comparison tool, which allows for gaps, can be used to detect weak
Results 1 - 10
of
60
