> Tag > Links tagged with 'bacterial genes'

Links tagged with 'bacterial genes'

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Found 17 links

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AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php [open in a new window]

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DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

links directory index: 70
TitlePublication YearGoogle Scholar Citation Count
AMIGene: Annotation of MIcrobial Genes200370
NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

antiSMASHTool Content

http://antismash.secondarymetabolites.org [open in a new window]

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DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences201119
NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

BROPResource Content

http://brop.org/ [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

links directory index: 101
TitlePublication YearGoogle Scholar Citation Count
The bioinformatics resource for oral pathogens200526
Comparative whole-genome analysis of virulent and avirulent strains of Porphyromonas gingivalis200475
NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

links directory index: 3211
TitlePublication YearGoogle Scholar Citation Count
The COG database: new developments in phylogenetic classification of proteins from complete genomes20011177
A genomic perspective on protein families19972034
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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

Comprehensive Microbial Resource (CMR)Database Content

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi [open in a new window]

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Model Organisms > Databases

The Comprehensive Microbial Resource provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
The comprehensive microbial resource201033
NAR Database Issue 2010
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tagsbacteria bacterial genes bacterial genome computational biology genetic databases nucleic acid databases protein databases tertiary protein structure

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl [open in a new window]

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DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways20088
NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

GeminaDatabase Content

http://gemina.igs.umaryland.edu [open in a new window]

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Model Organisms > Databases

The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database20107
NAR Database Issue 2010
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tagsanimals bacterial genes bacterial infections communicable diseases computational biology factual databases genetic databases humans nucleic acid databases viral genes virus diseases

GlimmerTool Content

http://cbcb.umd.edu/software/glimmer/ [open in a new window]

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DNA > Gene Prediction

Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.

links directory index: 2291
TitlePublication YearGoogle Scholar Citation Count
Identifying bacterial genes and endosymbiont DNA with Glimmer2007403
Improved microbial gene identification with GLIMMER19991199
Microbial gene identification using interpolated Markov models1998689
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external linksLink on Wikipedia
tagsalgorithms animals artifacts bacterial dna bacterial genes bacterial genome base sequence chromosome mapping decapodiformes dna sequence analysis genetic models genetic techniques haemophilus influenzae helicobacter pylori markov chains open reading frames prochloron reproducibility of results sensitivity and specificity sequence alignment symbiosis

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

links directory index: 714
TitlePublication YearGoogle Scholar Citation Count
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update20044
The web server of IBM's Bioinformatics and Pattern Discovery group20039
Dictionary-driven prokaryotic gene finding200241
Dictionary-driven protein annotation200237
The emergence of pattern discovery techniques in computational biology200092
Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.19990
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm1998531
NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

JProGOTool Content

http://www.jprogo.de/index.jsp [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information200626
NAR Web Server Issue 2006
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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

mGenomeSubtractorTool Content

http://bioinfo-mml.sjtu.edu.cn/mGS/ [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes201012
NAR Web Server Issue 2010
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tagsbacterial genes bacterial genome genomics oligonucleotide array sequence analysis sequence alignment species specificity

MICheckTool Content

http://www.genoscope.cns.fr/agc/tools/micheck/ [open in a new window]

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DNA > Annotations

MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes200515
NAR Web Server Issue 2005
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tagsbacterial genes bacterial genome genomics nucleic acid databases reproducibility of results time factors

MLSTTool Content

http://www.mlst.net/ [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

links directory index: 2035
TitlePublication YearGoogle Scholar Citation Count
The multilocus sequence typing network: mlst.net200589
Molecular typing of bacteria directly from cerebrospinal fluid200043
Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet1999136
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms19981767
NAR Web Server Issue 2005
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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

MobilomeFINDERTool Content

http://mml.sjtu.edu.cn/MobilomeFINDER/ [open in a new window]

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Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

links directory index: 83
TitlePublication YearGoogle Scholar Citation Count
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands200728
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria200645
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes200510
NAR Web Server Issue 2007
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tagsalgorithms bacterial genes bacterial genome bacterial rna computational biology enterobacteriaceae escherichia coli escherichia coli k12 fungal gene expression regulation genomic islands genomics oligonucleotide array sequence analysis polymerase chain reaction pseudomonas aeruginosa shigella shigella flexneri streptococcus suis theoretical models transfer rna

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

links directory index: 471
TitlePublication YearGoogle Scholar Citation Count
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes2006398
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA200373
NAR Web Server Issue 2006
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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

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