Bioinformatics. 2001 Dec;17(12):1179-82.

Taxonomy workbench.

Wildpaner M, Schneider G, Schleiffer A, Eisenhaber F.

Source

Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, A-1030 Vienna, Austria.

Abstract

At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database. AVAILABILITY: An implementation of the taxonomy workbench is accessible for public use as a www-service at http://mendel.imp.univie.ac.at/taxonomy/. Software components for the command-line and for the www-version are available on request. CONTACT: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at SUPPLEMENTARY INFORMATION: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html.

PMID:: 11751226; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. [Nucleic Acids Res. 2005]
PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets.
Novatchkova M, Wildpaner M, Schweizer D, Eisenhaber F. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W121-5.
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. [Bioinformatics. 2004]
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.
Cserzo M, Eisenhaber F, Eisenhaber B, Simon I. Bioinformatics. 2004 Jan 1; 20(1):136-7.
WILMA-automated annotation of protein sequences. [Bioinformatics. 2004]
WILMA-automated annotation of protein sequences.
Prlić A, Domingues FS, Lackner P, Sippl MJ. Bioinformatics. 2004 Jan 1; 20(1):127-8.
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis. [BMC Bioinformatics. 2003]
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis.
Badidi E, De Sousa C, Lang BF, Burger G. BMC Bioinformatics. 2003 Dec 16; 4:63. Epub 2003 Dec 16.
CDD: a Conserved Domain Database for protein classification. [Nucleic Acids Res. 2005]
CDD: a Conserved Domain Database for protein classification.
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, et al. Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D192-6.

See reviews... See all...

Cited by 1 PubMed Central article

Loss of the anaphase-promoting complex in quiescent cells causes unscheduled hepatocyte proliferation. [Genes Dev. 2004]
Loss of the anaphase-promoting complex in quiescent cells causes unscheduled hepatocyte proliferation.
Wirth KG, Ricci R, Giménez-Abián JF, Taghybeeglu S, Kudo NR, Jochum W, Vasseur-Cognet M, Nasmyth K. Genes Dev. 2004 Jan 1; 18(1):88-98.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.
Cited in Books
NCBI Bookshelf books that cite the current articles.

Recent activity

Clear Turn Off Turn On

Taxonomy workbench.
Taxonomy workbench.
Bioinformatics. 2001 Dec ;17(12):1179-82.

PubMed
A higher-order background model improves the detection of promoter regulatory el...
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.
Bioinformatics. 2001 Dec ;17(12):1113-22.

PubMed
Emphysematous lung destruction by cigarette smoke. The effects of latent adenovi...
Emphysematous lung destruction by cigarette smoke. The effects of latent adenoviral infection on the lung inflammatory response.
Am J Respir Cell Mol Biol. 2002 Jan ;26(1):52-7.

PubMed
Hypergastrinemia in response to gastric inflammation suppresses somatostatin.
Hypergastrinemia in response to gastric inflammation suppresses somatostatin.
Am J Physiol Gastrointest Liver Physiol. 2002 Jan ;282(1):G175-83.

PubMed
Effects of developmental exposure to lead, magnesium and zinc mixtures on spatia...
Effects of developmental exposure to lead, magnesium and zinc mixtures on spatial learning and expression of NMDA receptor subunit mRNA in Fischer 344 rats.
Toxicol Lett. 2002 Jan 25 ;126(2):107-19.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: