Published in Bioinformatics on May 01, 1999
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res (2007) 15.56
REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res (2001) 11.88
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol (2005) 11.82
Genome annotation assessment in Drosophila melanogaster. Genome Res (2000) 11.77
Annotating large genomes with exact word matches. Genome Res (2003) 11.07
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol (2004) 7.95
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A (2005) 4.46
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28
PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics (2007) 4.28
Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J Bacteriol (2004) 4.23
Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet (2006) 4.23
RSAT: regulatory sequence analysis tools. Nucleic Acids Res (2008) 3.93
Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics (2003) 2.94
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
A clustering method for repeat analysis in DNA sequences. Genome Biol (2001) 2.59
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet (2012) 2.44
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci U S A (2007) 2.35
Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol (2010) 2.22
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res (2002) 2.16
Extensive allelic variation among Francisella tularensis strains in a short-sequence tandem repeat region. J Clin Microbiol (2001) 2.03
The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol (2004) 1.97
The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res (2009) 1.75
Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics (2006) 1.65
Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics (2003) 1.65
A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS One (2007) 1.63
Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res (2002) 1.61
Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc Natl Acad Sci U S A (2003) 1.59
Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans. Genetics (2006) 1.48
Discrimination of human pathogenic subspecies of Francisella tularensis by using restriction fragment length polymorphism. J Clin Microbiol (2003) 1.38
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J Bacteriol (2009) 1.36
Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? Nucleic Acids Res (2002) 1.36
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res (2011) 1.33
Origin and fate of repeats in bacteria. Nucleic Acids Res (2002) 1.30
The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell (2003) 1.27
Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J Bacteriol (2006) 1.23
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics (2008) 1.22
An Eulerian path approach to local multiple alignment for DNA sequences. Proc Natl Acad Sci U S A (2005) 1.21
The genetic organization and evolution of the broad host range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa. Nucleic Acids Res (2001) 1.19
An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res (2003) 1.16
How repetitive are genomes? BMC Bioinformatics (2006) 1.16
Mastering seeds for genomic size nucleotide BLAST searches. Nucleic Acids Res (2003) 1.11
The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA. BMC Genomics (2009) 1.11
A single Banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus. J Virol (2008) 1.09
Swelfe: a detector of internal repeats in sequences and structures. Bioinformatics (2008) 1.06
A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella. PLoS Genet (2013) 1.05
Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics (2003) 1.05
MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Res (2000) 1.05
The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS One (2011) 1.03
The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biol (2010) 0.99
Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS One (2013) 0.98
Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PLoS One (2015) 0.97
VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res (2006) 0.97
Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids. PLoS One (2014) 0.97
Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22. BMC Genomics (2009) 0.96
Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS One (2013) 0.95
In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis. Plant Physiol (2003) 0.92
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus. ISME J (2012) 0.92
A new family of highly variable proteins in the Chlamydophila pneumoniae genome. Nucleic Acids Res (2002) 0.91
Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation. PLoS One (2011) 0.91
Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. BMC Genomics (2013) 0.89
TRStalker: an efficient heuristic for finding fuzzy tandem repeats. Bioinformatics (2010) 0.87
Suppression of repeat-mediated gross mitochondrial genome rearrangements by RecA in the moss Physcomitrella patens. Plant Cell (2009) 0.86
Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. BMC Bioinformatics (2003) 0.86
DNA loss at the Ceratocystis fimbriata mating locus results in self-sterility. PLoS One (2014) 0.85
Palindrome content of the yeast Saccharomyces cerevisiae genome. Curr Genet (2005) 0.84
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562. BMC Genomics (2008) 0.84
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection. Database (Oxford) (2015) 0.82
Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv. PLoS One (2014) 0.82
Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula. BMC Genomics (2007) 0.82
Simultaneous identification of long similar substrings in large sets of sequences. BMC Bioinformatics (2007) 0.82
The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions. Front Plant Sci (2016) 0.81
An algorithm for identifying novel targets of transcription factor families: application to hypoxia-inducible factor 1 targets. Cancer Inform (2009) 0.79
The complete chloroplast genome of colchicine plants (Colchicum autumnale L. and Gloriosa superba L.) and its application for identifying the genus. Planta (2015) 0.79
Ontology for genome comparison and genomic rearrangements. Comp Funct Genomics (2004) 0.77
Detecting key structural features within highly recombined genes. PLoS Comput Biol (2007) 0.77
Searching microsatellites in DNA sequences: approaches used and tools developed. Physiol Mol Biol Plants (2011) 0.77
The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene. PLoS One (2016) 0.76
The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses. Front Plant Sci (2017) 0.76
Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep (2016) 0.75
The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan). Physiol Mol Biol Plants (2016) 0.75
Plant MITEs: useful tools for plant genetics and genomics. Genomics Proteomics Bioinformatics (2003) 0.75
The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae), an Alpine Tibetan Herb. PLoS One (2016) 0.75
Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae). Front Plant Sci (2017) 0.75
The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales. Front Plant Sci (2017) 0.75
Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences. Genetica (2017) 0.75
Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. Bot Stud (2017) 0.75
Chloroplast genome structures in Gentiana (Gentianaceae), based on three medicinal alpine plants used in Tibetan herbal medicine. Curr Genet (2016) 0.75
REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res (2001) 11.88
Computation and visualization of degenerate repeats in complete genomes. Proc Int Conf Intell Syst Mol Biol (2000) 2.34
GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol (1996) 1.56