Published in Nucleic Acids Res on January 11, 1984
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
A new method for predicting signal sequence cleavage sites. Nucleic Acids Res (1986) 37.19
Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26
MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res (1995) 21.22
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res (1987) 14.53
Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci U S A (1989) 14.45
Analysis of E. coli promoter sequences. Nucleic Acids Res (1987) 14.12
Sequence and characteristics of IS900, an insertion element identified in a human Crohn's disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res (1989) 6.92
Precise insertion of antibiotic resistance determinants into Tn21-like transposons: nucleotide sequence of the OXA-1 beta-lactamase gene. Proc Natl Acad Sci U S A (1987) 5.28
Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. EMBO J (1986) 5.20
Intron splicing: a conserved internal signal in introns of animal pre-mRNAs. Proc Natl Acad Sci U S A (1984) 4.71
Conserved and variable functions of the sigmaE stress response in related genomes. PLoS Biol (2006) 4.46
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Regulated expression of early and late RNAs and proteins from the human cytomegalovirus immediate-early gene region. J Virol (1989) 3.98
The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res (1993) 3.60
Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res (2005) 3.49
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol (2004) 3.15
Nucleotide sequence of the cell wall proteinase gene of Streptococcus cremoris Wg2. Appl Environ Microbiol (1988) 3.11
A gene in the chromosomal region 3p21 with greatly reduced expression in lung cancer is similar to the gene for ubiquitin-activating enzyme. Proc Natl Acad Sci U S A (1993) 3.09
Isolation and characterization of genes encoding two chitinase enzymes from Serratia marcescens. EMBO J (1986) 3.08
Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02
Domain enhanced lookup time accelerated BLAST. Biol Direct (2012) 2.87
A biophysical approach to transcription factor binding site discovery. Genome Res (2003) 2.62
Primary structure and differential expression of glutamine synthetase genes in nodules, roots and leaves of Phaseolus vulgaris. EMBO J (1986) 2.59
Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. Nucleic Acids Res (1985) 2.56
Training back-propagation neural networks to define and detect DNA-binding sites. Nucleic Acids Res (1991) 2.47
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs. Nucleic Acids Res (1985) 2.35
A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res (2001) 2.21
A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol (2007) 2.15
The nucleotide sequence of the uvrD gene of E. coli. Nucleic Acids Res (1984) 2.14
A precise map of splice junctions in the mRNAs of minute virus of mice, an autonomous parvovirus. J Virol (1986) 2.11
Analysis of donor splice sites in different eukaryotic organisms. J Mol Evol (1997) 2.09
Detection of multiple, novel reverse transcriptase coding sequences in human nucleic acids: relation to primate retroviruses. J Virol (1989) 2.05
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucleic Acids Res (1994) 2.04
Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J Bacteriol (1996) 1.97
A survey of motif discovery methods in an integrated framework. Biol Direct (2006) 1.94
A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res (1988) 1.93
Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci U S A (2005) 1.93
Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol (2004) 1.93
Analysis of the occurrence of promoter-sites in DNA. Nucleic Acids Res (1986) 1.86
Reduced heat resistance of mutant spores after cloning and mutagenesis of the Bacillus subtilis gene encoding penicillin-binding protein 5. J Bacteriol (1986) 1.83
Identification and sequence of the gene for abequose synthase, which confers antigenic specificity on group B salmonellae: homology with galactose epimerase. J Bacteriol (1989) 1.71
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res (2007) 1.71
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res (1997) 1.69
Conservation versus parallel gains in intron evolution. Nucleic Acids Res (2005) 1.67
Genomic sequence for human prointerleukin 1 beta: possible evolution from a reverse transcribed prointerleukin 1 alpha gene. Nucleic Acids Res (1986) 1.66
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
The cloning and expression of the aroL gene from Escherichia coli K12. Purification and complete amino acid sequence of shikimate kinase II, the aroL-gene product. Biochem J (1986) 1.60
The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.). Nucleic Acids Res (1985) 1.58
Probabilistic inference of transcription factor binding from multiple data sources. PLoS One (2008) 1.58
The next generation of transcription factor binding site prediction. PLoS Comput Biol (2013) 1.55
Nucleotide sequence of a cluster of Escherichia coli enterobactin biosynthesis genes: identification of entA and purification of its product 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase. J Bacteriol (1989) 1.54
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Adaptation of Xanthobacter autotrophicus GJ10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element IS1247. J Bacteriol (1995) 1.44
Molecular analysis of the asense gene, a member of the achaete-scute complex of Drosophila melanogaster, and its novel role in optic lobe development. EMBO J (1989) 1.44
Defining the consensus sequences of E.coli promoter elements by random selection. Nucleic Acids Res (1988) 1.44
Tnni3k modifies disease progression in murine models of cardiomyopathy. PLoS Genet (2009) 1.44
MotX, the channel component of the sodium-type flagellar motor. J Bacteriol (1994) 1.43
Vaccinia virus encodes two proteins that are structurally related to members of the plasma serine protease inhibitor superfamily. J Virol (1989) 1.40
Escherichia coli possesses two homologous anaerobic C4-dicarboxylate membrane transporters (DcuA and DcuB) distinct from the aerobic dicarboxylate transport system (Dct). J Bacteriol (1994) 1.37
MBIS--an integrated system for the retrieval and analyses of sequence data from nucleic acids and proteins. Nucleic Acids Res (1986) 1.37
A novel approach to describe a U1 snRNA binding site. Nucleic Acids Res (2003) 1.35
Neural network detects errors in the assignment of mRNA splice sites. Nucleic Acids Res (1990) 1.35
A method to locate protein coding sequences in DNA of prokaryotic systems. Nucleic Acids Res (1985) 1.34
Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res (2010) 1.33
The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res (1996) 1.32
Finding errors in DNA sequences. Proc Natl Acad Sci U S A (1992) 1.30
A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics (2005) 1.28
The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics (2006) 1.26
Molecular analysis of the 3,6-dideoxyhexose pathway genes of Yersinia pseudotuberculosis serogroup IIA. J Bacteriol (1993) 1.25
Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc Natl Acad Sci U S A (2010) 1.23
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res (2005) 1.22
A Drosophila CREB/CREM homolog encodes multiple isoforms, including a cyclic AMP-dependent protein kinase-responsive transcriptional activator and antagonist. Mol Cell Biol (1995) 1.21
An assessment of neural network and statistical approaches for prediction of E. coli promoter sites. Nucleic Acids Res (1992) 1.21
A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18
DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors. Biochem J (1988) 1.16
Prediction of splice junctions in mRNA sequences. Nucleic Acids Res (1985) 1.14
Sequence analysis of the Lactococcus lactis temperate bacteriophage BK5-T and demonstration that the phage DNA has cohesive ends. Appl Environ Microbiol (1995) 1.13
Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. J Bacteriol (1989) 1.12
A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics (2009) 1.12
Discovering structural correlations in alpha-helices. Protein Sci (1994) 1.10
Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res (2013) 1.09
A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J Bacteriol (1995) 1.08
Isolation and characterization of a low-abundance splice variant from the human cytomegalovirus major immediate-early gene region. J Virol (1995) 1.05
FITBAR: a web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics (2010) 1.05
The sequence of the distal end of the E. coli ribosomal RNA rrnE operon indicates conserved features are shared by rrn operons. Nucleic Acids Res (1985) 1.05
Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol (2013) 1.04
Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02
Quantitative sequence-activity models (QSAM)--tools for sequence design. Nucleic Acids Res (1993) 1.02
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol Syst Biol (2013) 1.02
Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics (2013) 1.01
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res (2010) 1.01
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons. Nucleic Acids Res (2006) 1.01
Molecular characterization of promoters of the Lactococcus lactis subsp. cremoris temperate bacteriophage BK5-T and identification of a phage gene implicated in the regulation of promoter activity. Appl Environ Microbiol (1990) 1.00
Molecular and cellular characterization of the 29-kilodalton peripheral membrane protein of Entamoeba histolytica: differentiation between pathogenic and nonpathogenic isolates. Infect Immun (1992) 0.99
Method of predicting splice sites based on signal interactions. Biol Direct (2006) 0.98
Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res (2004) 0.96
Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics (2008) 0.96
A catalogue of splice junction sequences. Nucleic Acids Res (1982) 39.41
Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res (1983) 38.72
Translational initiation in prokaryotes. Annu Rev Microbiol (1981) 18.46
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res (1982) 9.99
Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci U S A (1979) 9.28
The nucleotide sequence of the human beta-globin gene. Cell (1980) 8.11
Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd. Proc Natl Acad Sci U S A (1975) 7.14
Sequences of the recA gene and protein. Proc Natl Acad Sci U S A (1980) 6.87
Bacteriophage T7 early promoters: nucleotide sequences of two RNA polymerase binding sites. J Mol Biol (1975) 6.52
The relationship between function and DNA sequence in an intercistronic regulatory region in phage lambda. Nature (1978) 5.38
DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation. Nature (1978) 5.31
Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans. Nature (1981) 5.30
Spacer mutations in the lac ps promoter. Proc Natl Acad Sci U S A (1982) 5.19
Interaction of RNA polymerase with promoters from bacteriophage fd. Eur J Biochem (1977) 4.94
Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci U S A (1980) 4.90
DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli. Cell (1979) 4.39
The E. coli beta-lactamase attenuator mediates growth rate-dependent regulation. Nature (1981) 4.20
The ovalbumin gene family: structure of the X gene and evolution of duplicated split genes. Cell (1980) 4.14
Sequence determinants of promoter activity. Cell (1982) 4.00
Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res (1983) 3.81
5'-Terminal nucleotide sequence of Escherichia coli lactose repressor mRNA: features of translational initiation and reinitiation sites. Proc Natl Acad Sci U S A (1977) 3.14
Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli. Cell (1979) 3.00
A lac promoter with a changed distance between -10 and -35 regions. Nucleic Acids Res (1982) 2.97
A possible novel interaction between the 3'-end of 18 S ribosomal RNA and the 5'-leader sequence of many eukaryotic messenger RNAs. FEBS Lett (1982) 2.91
Promoter mutations in the transfer RNA gene tyrT of Escherichia coli. Proc Natl Acad Sci U S A (1979) 2.89
Sequence of promoter for coat protein gene of bacteriophage fd. Nature (1976) 2.82
Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance. Biochemistry (1981) 2.67
Promoter for the establishment of repressor synthesis in bacteriophage lambda. Proc Natl Acad Sci U S A (1980) 2.23
Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant. J Bacteriol (1980) 2.13
Nucleotide sequence of an Escherichia coli tRNA (Leu 1) operon and identification of the transcription promoter signal. Nucleic Acids Res (1981) 2.10
Sequence and organization of the human mitochondrial genome. Nature (1981) 57.39
Sequence data handling by computer. Nucleic Acids Res (1977) 45.33
A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res (1980) 36.42
A strategy of DNA sequencing employing computer programs. Nucleic Acids Res (1979) 19.82
Further procedures for sequence analysis by computer. Nucleic Acids Res (1978) 18.94
A computer program to search for tRNA genes. Nucleic Acids Res (1980) 17.12
Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res (1982) 14.73
An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res (1982) 12.58
A new DNA sequence assembly program. Nucleic Acids Res (1995) 12.03
Nucleotide sequence of bacteriophage G4 DNA. Nature (1978) 10.46
Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res (1982) 9.99
Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. Nucleic Acids Res (1984) 6.38
Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res (1984) 6.08
The C. elegans genome sequencing project: a beginning. Nature (1992) 5.36
A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res (1991) 5.03
The current status and portability of our sequence handling software. Nucleic Acids Res (1986) 4.54
Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci U S A (1980) 3.74
Software for genome mapping by fingerprinting techniques. Comput Appl Biosci (1988) 3.67
Nucleotide sequence homology at 12 intron--exon junctions in the chick ovalbumin gene. Nature (1978) 3.30
A computer program to enter DNA gel reading data into a computer. Nucleic Acids Res (1984) 3.21
Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance. Biochemistry (1981) 2.67
A method for measuring the non-random bias of a codon usage table. Nucleic Acids Res (1984) 2.57
Experiment files and their application during large-scale sequencing projects. DNA Seq (1996) 2.48
A standard file format for data from DNA sequencing instruments. DNA Seq (1992) 2.42
Searching for patterns in protein and nucleic acid sequences. Methods Enzymol (1990) 2.39
Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes. J Gen Virol (1989) 2.13
The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res (1995) 1.79
Both DNA strands of antibody genes are hypermutation targets. Proc Natl Acad Sci U S A (1998) 1.77
Sequence of three introns in the chick ovalbumin gene. Nature (1979) 1.69
Automated detection of point mutations using fluorescent sequence trace subtraction. Nucleic Acids Res (1998) 1.67
Finding protein coding regions in genomic sequences. Methods Enzymol (1990) 1.61
Polar zippers. Curr Biol (1993) 1.48
An X windows and UNIX implementation of our sequence analysis package. Comput Appl Biosci (1991) 1.26
An oligo-screening strategy to fill gaps found during shotgun sequencing projects. DNA Seq (1998) 1.14
Protein disk of tobacco mosaic virus at 2.8 A resolution showing the interactions within and between subunits. Nature (1978) 1.04
Computer methods to aid the determination and analysis of DNA sequences. Biochem Soc Trans (1984) 0.84