Profile hidden Markov models.

RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol (2011) 28.61

An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81

bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes (2007) 25.13

Pfam: the protein families database. Nucleic Acids Res (2013) 22.48

The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68

TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res (2001) 20.84

GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88

CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54

GeneWise and Genomewise. Genome Res (2004) 17.87

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99

The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59

The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32

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

The Comprehensive Microbial Resource. Nucleic Acids Res (2001) 11.19

The PredictProtein server. Nucleic Acids Res (2004) 10.89

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics (2002) 10.84

The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03

TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83

Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72

Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell (2003) 7.66

Using GeneWise in the Drosophila annotation experiment. Genome Res (2000) 7.50

Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res (2004) 7.39

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell (2004) 7.11

The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res (2004) 6.72

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res (2006) 6.59

Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res (2001) 6.49

The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36

An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A (2005) 6.26

Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci U S A (2003) 6.01

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94

GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res (2003) 5.90

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70

HMM Logos for visualization of protein families. BMC Bioinformatics (2004) 5.69

Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys J (2006) 5.52

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci (2009) 5.50

A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47

ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res (2004) 5.44

Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol (2010) 5.33

Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res (2008) 5.12

A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One (2013) 5.10

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75

From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol (2002) 4.66

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res (2006) 4.64

Genome re-annotation: a wiki solution? Genome Biol (2007) 4.61

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics (2002) 4.49

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol (2011) 4.45

Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A (2008) 4.37

The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18

RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14

Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08

Assessing the gene space in draft genomes. Nucleic Acids Res (2008) 4.03

Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell (2008) 4.00

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res (2006) 3.99

Predicting active site residue annotations in the Pfam database. BMC Bioinformatics (2007) 3.95

Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell (2002) 3.91

Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell (2003) 3.80

A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res (2002) 3.76

Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics (2004) 3.68

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics (2011) 3.64

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. Stand Genomic Sci (2011) 3.62

Protein subfamily assignment using the Conserved Domain Database. BMC Res Notes (2008) 3.62

Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet (2009) 3.60

Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform Online (2008) 3.57

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res (2000) 3.56

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52

Systematic identification of novel protein domain families associated with nuclear functions. Genome Res (2002) 3.50

The PEDANT genome database. Nucleic Acids Res (2003) 3.47

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol (2006) 3.45

The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res (2006) 3.45

Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J Bacteriol (2006) 3.40

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res (2005) 3.28

Using the Acropora digitifera genome to understand coral responses to environmental change. Nature (2011) 3.26

The G protein-coupled receptor repertoires of human and mouse. Proc Natl Acad Sci U S A (2003) 3.24

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics (2005) 3.23

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genet (2010) 3.03

Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol (2005) 2.99

Profile Comparer: a program for scoring and aligning profile hidden Markov models. Bioinformatics (2008) 2.94

Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res (2004) 2.91

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res (2003) 2.91

Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol (2003) 2.90

Prp8 protein: at the heart of the spliceosome. RNA (2005) 2.89

A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89

Structure and signaling mechanism of Per-ARNT-Sim domains. Structure (2009) 2.86

A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics (2009) 2.85

Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun (2012) 2.84

MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics (2006) 2.81

Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet (2010) 2.77

Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res (2007) 2.75

RXLR-mediated entry of Phytophthora sojae effector Avr1b into soybean cells does not require pathogen-encoded machinery. Plant Cell (2008) 2.72

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72

Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res (2004) 2.66