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Links tagged with 'bacteria'

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Found 19 links

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AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html [open in a new window]

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Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
AHMII: Agent to Help Microbial Information Integration.20030
NAR Web Server Issue 2003
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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

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

Argonne National Laboratory - Computational Biology DatabasesTool Content

http://www-unix.mcs.anl.gov/compbio/index.html [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.

links directory index: 833
TitlePublication YearGoogle Scholar Citation Count
Sentra, a database of signal transduction proteins200216
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction2000369
MPW: the Metabolic Pathways Database1998127
Searching for patterns in genomic data1997221
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database1996100
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tagsanimals bacteria biological transport chemotaxis conserved sequence enzymes eukaryota factual databases fungi genome humans metabolism methylation multigene family open reading frames phosphorylation prokaryotic cells protein databases protein kinases protein-serine-threonine kinases proteins sequence homology signal transduction systems integration tertiary protein structure

BAGETTool Content

http://archaea.u-psud.fr/bin/baget.dll [open in a new window]

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Model Organisms > Microbes

BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction of specific gene and protein sequences from completely determined prokaryotic genomes. Query results can be exported as a rich text format file for printing, archival or further analysis.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence20087
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tagsarchaea bacteria database management systems genetic databases proteome sequence analysis

BioMart CentralDatabase Content

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

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DNA > DNA and Genomic Analysis
Human Genome > Other Resources
Model Organisms > Databases
Protein > Proteomics

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-database searches that might otherwise require several complicated steps.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
BioMart Central Portal: an open database network for the biological community20119
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tagsanimals bacteria biomedical research database management systems factual databases fungi genome humans international cooperation viruses

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

cpnDBDatabase Content

http://www.cpndb.ca/cpnDB/home.php [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Data
Protein > Sequence Retrieval

cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
cpnDB: a chaperonin sequence database200473
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tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/ [open in a new window]

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Model Organisms > Databases

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system20119
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals bacteria binding sites drosophila drosophila proteins genetic databases transcription factors transcriptional regulatory elements two-hybrid system techniques

FMMTool Content

http://FMM.mbc.nctu.edu.tw/ [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
FMM: a web server for metabolic pathway reconstruction and comparative analysis200911
NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

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

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

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/ [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

links directory index: 127
TitlePublication YearGoogle Scholar Citation Count
MetaPath Online: a web server implementation of the network expansion algorithm200722
Evolutionary changes of metabolic networks and their biosynthetic capacities200614
Hierarchy of metabolic compounds based on their synthesising capacity20069
Expanding metabolic networks: scopes of compounds, robustness, and evolution200582
A cross species comparison of metabolic network functions.20050
Structural analysis of expanding metabolic networks.20040
NAR Web Server Issue 2007
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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

MicrobesOnlineDatabase Content

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

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Model Organisms > Databases

MicrobesOnline portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources.

links directory index: 82
TitlePublication YearGoogle Scholar Citation Count
MicrobesOnline: an integrated portal for comparative and functional genomics201082
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsalgorithms bacteria bacterial genome computational biology gene expression profiling genetic databases nucleic acid databases oligonucleotide array sequence analysis protein databases tertiary protein structure

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