> Tag > Links tagged with 'archaea'

Links tagged with 'archaea'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 8 links

Displaying 8 links

Resources (0)Hide Databases (4)Hide Tools (4)

BAGETTool Content

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

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsarchaea bacteria database management systems genetic databases proteome sequence analysis

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/ [open in a new window]

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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/ [open in a new window]

Share This Link
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.

links directory index: 79
TitlePublication YearGoogle Scholar Citation Count
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges20121
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations201078
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs animals archaea bacterial genome computational biology fishes genetic databases humans nucleic acid databases primates protein databases rats tertiary protein structure

JProGOTool Content

http://www.jprogo.de/index.jsp [open in a new window]

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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]

Share This Link
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
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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/ [open in a new window]

Share This Link
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.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
The MiST2 database: a comprehensive genomics resource on microbial signal transduction201035
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
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/ [open in a new window]

Share This Link
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.

links directory index: 1063
TitlePublication YearGoogle Scholar Citation Count
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy20031063
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals archaea archaeal rna bacteria bacterial rna eukaryotic cells nucleic acid databases phylogeny prokaryotic cells ribosomal rna rna sequence analysis sequence alignment

TADBDatabase Content

http://bioinfo-mml.sjtu.edu.cn/TADB/ [open in a new window]

Share This Link
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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea201114
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsarchaea archaeal genome archaeal proteins bacteria bacterial genome bacterial proteins bacterial toxins biological toxins genetic databases genetic loci

Associated Tag Cloud