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Links tagged with 'bacterial dna'

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Found 16 links

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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

CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

NAR Web Server Issue 2007
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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

FeatureScanTool Content

http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Similarity Searching

FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.

NAR Web Server Issue 2006
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tagsanimals automated pattern recognition bacterial dna bacterial genes dna dna sequence analysis escherichia coli genetic models genetic promoter regions genomics humans mice nucleic acid sequence homology rats sequence alignment thermodynamics

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

NAR Web Server Issue 2003NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

GlimmerTool Content

http://cbcb.umd.edu/software/glimmer/

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.

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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

Intergr8Tool Content

http://www.ebi.ac.uk/integr8/

Human Genome > Other Resources
Model Organisms > General Resources

Integr8 is a browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.

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tagsarchaeal dna bacterial dna genetic databases genomics proteomics systems integration

Interolog/Regulog DatabaseDatabase Content

http://interolog.gersteinlab.org/

Model Organisms > Fly
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

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tagsamino acid sequence amino acid sequence homology animals bacterial dna bacterial genome bacterial proteins binding sites caenorhabditis elegans caenorhabditis elegans proteins computational biology conserved sequence dna dna-binding proteins drosophila melanogaster drosophila proteins fungal dna fungal genome genome helicobacter pylori helminth dna protein binding protein databases protein interaction mapping proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org

DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

NAR Web Server Issue 2010
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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

MLSTTool Content

http://www.mlst.net/

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.

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

mrepsTool Content

http://bioinfo.lifl.fr/mreps/

DNA > Structure and Sequence Feature Detection

mreps is a tool for identifing tandemn repeats in DNA sequences.

NAR Web Server Issue 2003
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tagsalgorithms bacterial dna bacterial genes dna dna sequence analysis genetic polymorphism genomics human genome humans neisseria meningitidis saccharomyces cerevisiae tandem repeat sequences

Pseudomonas Genome DatabaseDatabase Content

http://www.pseudomonas.com

Model Organisms > Databases

The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.

This content is being maintained by fionabrinkman.

NAR Database Issue 2011
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tagsbacterial dna bacterial gene expression regulation bacterial genes bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genetic polymorphism genomic islands genomics human genome humans microbial drug resistance molecular sequence data pseudomonas pseudomonas aeruginosa pseudomonas infections species specificity systems integration voluntary workers

Pseudomonas Genome ProjectDatabase Content

http://pseudomonas.com/

Model Organisms > Microbes

This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information.

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tagsbacterial dna bacterial gene expression regulation bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genomics humans microbial drug resistance molecular sequence data pseudomonas aeruginosa pseudomonas infections species specificity systems integration

REPKTool Content

http://rocaplab.ocean.washington.edu/tools/repk

DNA > Tools For the Bench
Model Organisms > Microbes

REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.

NAR Web Server Issue 2007
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tagsalgorithms bacteria bacterial dna computational biology ecosystem enzymes factual databases microbiology phylogeny restriction fragment length polymorphism ribosomal dna ribosomal rna

TFAMTool Content

http://tfam.lcb.uu.se/

RNA > Functional RNAs

TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.

NAR Web Server Issue 2007
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tagsalphaproteobacteria animals bacterial dna bacterial genome computational biology drosophila melanogaster genetic variation genomics histidine-trna ligase horizontal gene transfer molecular evolution nucleic acid databases phylogeny statistical models transfer rna