PHOG-BLAST--a new generation tool for fast similarity search of protein families.

PubWeight™: 0.91‹?›

🔗 View Article (PMC 1522020)

Published in BMC Evol Biol on June 22, 2006

Authors

Igor V Merkeev1, Andrey A Mironov

Author Affiliations

1: State Scientific Center GosNIIGenetica, 1st Dorozhny pr,, 1, Moscow, 113545, Russia. imerkeev@mail.ru

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Basic local alignment search tool. J Mol Biol (1990) 659.07

Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60

Identification of common molecular subsequences. J Mol Biol (1981) 130.53

Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33

The Pfam protein families database. Nucleic Acids Res (2004) 56.46

The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84

Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci (1994) 31.96

Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26

Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10

Position-based sequence weights. J Mol Biol (1994) 24.41

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci (1996) 19.74

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A (1994) 18.46

Touring protein fold space with Dali/FSSP. Nucleic Acids Res (1998) 18.00

Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc Natl Acad Sci U S A (1993) 17.71

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics (1999) 12.64

Weights for data related by a tree. J Mol Biol (1989) 12.63

Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89

Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J Mol Biol (1990) 11.50

Using substitution probabilities to improve position-specific scoring matrices. Comput Appl Biosci (1996) 11.32

Automated assembly of protein blocks for database searching. Nucleic Acids Res (1991) 10.84

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35

Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci (2000) 6.23

Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res (1996) 5.68

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol (2002) 4.99

PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng (1999) 4.59

Orthologs and paralogs - we need to get it right. Genome Biol (2001) 1.95

Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71

An apology for orthologs - or brave new memes. Genome Biol (2001) 1.35

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics (2005) 1.02

PHOG: a database of supergenomes built from proteome complements. BMC Evol Biol (2006) 0.88

Articles by these authors

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem (2002) 4.33

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem (2003) 3.15

Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet (2004) 3.14

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res (2002) 2.84

Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. Proc Natl Acad Sci U S A (2003) 2.61

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res (2003) 1.98

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res (2006) 1.95

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res (2004) 1.94

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci (2004) 1.91

Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol (2012) 1.89

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA (2003) 1.89

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81

A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res (2004) 1.57

Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res (2006) 1.13

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol (2010) 1.11

Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria. FEMS Microbiol Lett (2003) 1.10

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics (2007) 1.10

Evolution of prokaryotic genes by shift of stop codons. J Mol Evol (2010) 0.97

Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol (2007) 0.92

Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene (2002) 0.89

PHOG: a database of supergenomes built from proteome complements. BMC Evol Biol (2006) 0.88

Exact mapping of prokaryotic gene starts. Brief Bioinform (2002) 0.82

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res (2012) 0.82

Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One (2012) 0.82

Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. BMC Evol Biol (2009) 0.82

Hidden Markov models for evolution and comparative genomics analysis. PLoS One (2013) 0.77

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. Bioinformatics (2013) 0.77

Compensatory evolution of intrinsic transcription terminators in Bacillus cereus. Genome Biol Evol (2017) 0.75

Two genetic algorithms for identification of regulatory signals. In Silico Biol (2003) 0.75