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Links tagged with 'archaea'

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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

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

eggNOGDatabase Content

http://eggnog.embl.de/version_2/

Protein > Databases

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).s (built from 2,590,259 proteins) and provides a broad functional description for at least 1,966,709 (88%) of them.

NAR Database Issue 2010
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tagsamino acid motifs animals archaea bacterial genome computational biology fishes genetic databases humans nucleic acid databases primates protein databases rats tertiary protein structure

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

JProGOTool Content

http://www.jprogo.de/index.jsp

Expression > Transcript Expression Analysis
Model Organisms > Microbes

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

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/

Other Molecules > Metabolites
Protein > Interactions, Pathways, 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.

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

MiSTDatabase Content

http://genomics.ornl.gov/mist/

Model Organisms > Databases
Protein > Databases

The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface.

NAR Database Issue 2010
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins computational biology genetic databases protein databases signal transduction tertiary protein structure

Ribosomal Database ProjectDatabase Content

http://rdp.cme.msu.edu/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
RNA > Functional RNAs
RNA > Sequence Retrieval

Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.

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tagsanimals archaea archaeal rna bacteria bacterial rna eukaryotic cells nucleic acid databases phylogeny prokaryotic cells ribosomal rna rna sequence analysis sequence alignment

RNAzTool Content

http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.

NAR Web Server Issue 2007
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tagsalgorithms archaea base sequence computational biology consensus sequence conserved sequence escherichia coli genome molecular evolution molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny prokaryotic cells ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis rna stability sequence alignment thermodynamics untranslated rna

TADBDatabase Content

http://bioinfo-mml.sjtu.edu.cn/TADB/

Other Molecules > Databases

TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB.

NAR Database Issue 2011
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tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins bacterial toxins biological toxins genetic databases genetic loci