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Links tagged with 'bacteria'

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Found 24 links

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AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html

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.

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

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.

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

BAGETTool Content

http://archaea.u-psud.fr/bin/baget.dll

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.

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tagsarchaea bacteria database management systems genetic databases proteome sequence analysis

BROPResource Content

http://brop.org/

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.

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

CMRDatabase Content

http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.

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tagsbacteria bacterial genes bacterial genome factual databases information services

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

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.

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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

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.

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

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.

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tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

CRISPRcomparTool Content

http://crispr.u-psud.fr/CRISPRcompar/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.

NAR Web Server Issue 2008
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tagsalleles bacteria bacterial typing techniques tandem repeat sequences

CVTreeTool Content

http://tlife.fudan.edu.cn/cvtree

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

NAR Web Server Issue 2004NAR Web Server Issue 2009
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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/

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.

NAR Database Issue 2011
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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/

Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

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

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.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

InsigniaTool Content

http://insignia.cbcb.umd.edu

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.

NAR Web Server Issue 2009
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tagsanimals bacteria bacterial genome dna sequence analysis humans infection viral genome viruses

IslandPathTool Content

http://www.pathogenomics.sfu.ca/islandpath/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin.

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tagsarchaea archaeal genome bacteria bacterial genome cpg islands database management systems dna sequence analysis horizontal gene transfer phylogeny sequence alignment