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Microbes

This section contain links to microbial genome resources including: genome sequences, annotations and comparative analyses.

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Found 58 links

Displaying 15 links

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

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

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

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

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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ATIVSTool Content

http://influenza.nhri.org.tw/ATIVS/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.

This content is being maintained by Jade.

NAR Web Server Issue 2009
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tagsantigenic variation h3n2 subtype influenza a virus human influenza humans influenza virus hemagglutinin glycoproteins orthomyxoviridae population surveillance sequence analysis viral antibodies viral antigens

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

NAR Web Server Issue 2006
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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

NAR Web Server Issue 2010
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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

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

BASysTool Content

http://basys.ca

DNA > Annotations
Model Organisms > Microbes

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

This content is being maintained by gary.vandomselaar@gmail.com.

NAR Web Server Issue 2005
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tagsbacterial chromosomes bacterial genome genomics plasmids

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

CGView ServerTool Content

http://stothard.afns.ualberta.ca/cgview_server/

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.

This content is being maintained by jason.grant.

NAR Web Server Issue 2008
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tagsbacterial genome chloroplast genome chromosome mapping circular dna genomics mitochondrial genome plasmids sequence alignment

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

CPA - Comparative Pathway AnalyzerTool Content

https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html

Expression > Networks
Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.

NAR Web Server Issue 2008
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tagscluster analysis factual databases metabolic networks and pathways

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

CRISPRFinderTool Content

http://crispr.u-psud.fr/Server/CRISPRfinder.php

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

NAR Web Server Issue 2007
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tagsalgorithms archaeal genome bacterial genome chromosome mapping computational biology database management systems genetic databases intergenic dna nucleic acid repetitive 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

Tags associated with subcategory 'Model Organisms/Microbes'

bacterial genome genomics bacteria bacterial genes algorithms sequence alignment dna sequence analysis phylogeny computational biology genetic databases humans archaeal genome bacterial proteins open reading frames viruses animals plasmodium falciparum conserved sequence protein conformation protozoan proteins fos genes dna footprinting metallothionein multigene family myc genes nucleic acid sequence homology introns interleukin-3 fish proteins viral genome genetic promoter regions insulin growth hormone chloroplast dna genome secondary protein structure archaeal genes bacillus anthracis computer-aided design proteome membrane proteins rats prokaryotic initiation factors protein biosynthesis metabolic networks and pathways translational peptide chain initiation dna probes equipment design hiv-1 markov chains tertiary protein structure fungal genome regulator genes genetic recombination dna breaks oligonucleotide array sequence analysis ribosomal rna rrna genes base sequence staphylococcus aureus enterobacteriaceae transcriptional regulatory elements polymerase chain reaction serotyping streptococcus pneumoniae human influenza pneumococcal meningitis nucleic acid databases meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis influenza virus hemagglutinin glycoproteins orthomyxoviridae escherichia coli proteins molecular evolution protein sequence analysis virulence chromosome mapping online systems population surveillance sequence analysis viral antibodies gene expression profiling viral antigens gene frequency evaluation studies as topic gene deletion nucleic acid regulatory sequences nucleotidyltransferases salmonella gene components escherichia coli isoelectric point molecular weight proteins proteomics fungi microbiological techniques bacterial meningitis bacterial typing techniques