Bioinformatic Harvester

The Bioinformatics Harvester (English harvester, " the harvester employees ") is a bioinformatic meta search engine on genes and proteins from human, mouse, zebrafish, Arabidopsis, Drosophila and rat. The harvester combines, or linked to the content of about 51 bioinformatics resources is often used. A special ranking algorithm sorts the information in advance and presented to the user the most relevant search results in a very short time.

Operation

The Harvester collects information from Protein-/Gen-Datenbanken and so-called prediction or prediction servers. For this, the Harvester simulates a human user, invokes the corresponding external database page and stores them on local hard drives. As a basis for collecting the information was for the UniProt protein database of Uniprot Consortium, and the IPI database (international protein index). The Harvester collection currently includes:

  • Man: about 72,000 pages
  • Mouse: approx 54,000 pages
  • Rat: 41,000 pages
  • Zebrafish: 45,000 pages
  • Arabidopsis: 34,000 pages
  • Drosophila: 33,000 pages

Bioinformatics information

The Harvester Search combines the following bioinformatic information:

Text-based information

Of ... the following databases:

  • Uniprot, world's largest protein database
  • SOURCE clear representation of genetic information
  • Simple Modular Architecture Research Tool ( SMART),
  • Sosui examined transmembrane domains
  • PSORT, prediction of protein localization
  • HomoloGene, comparing proteins from different species
  • Gfp cdna, protein localization by fluorescence microscopy
  • International Protein Index ( IPI).
  • OMIM Comprehensive database of gene changes in human

Databases rich with graphic elements

These databases are not " collected ", but linked in so-called inline frames. Inline frames are a type of transparent window in an HTML page. Through this window you can " see through " in real time to appropriate external databases. Several such inline frame windows are combined on a Harvester protein page. This method allows to consider all information from the various databases at a glance and compare.

Currently, the following server using inline frame are combined at the Harvester pages:

  • NCBI -BLAST finds local sequence similarities
  • Conserved Domain Database is protein domains of known function
  • Mouse Genome Informatics. Description gene and phenotype information of the mouse
  • German Resource Center for Genome Research ( RZPD ) in Berlin / Heidelberg
  • STRING server for the representation of interacting genes and proteins at the EMBL
  • IHOP, linked literature ( PubMed) with the help of gene and protein synonyms
  • ZFIN, zebrafish specific database

Link outs

Link outs link to external search engines or bioinformatics service facilities.

  • Genome Browser, clear presentation of current genomes of the University of California, Santa Cruz
  • Mitocheck, fluorescence movies of siRNA experiments in cell cultures
  • Entrez Gene, meta-search engine of the National Center for Biotechnology
  • PolyMeta, Metasuchemaschine through PubMed, Scirus and other sources of Scientific Publications
  • Google Scholar, Google's literature search
  • LOCATE subcellular protein localization database ( mouse)
Ensembl Frederick Sanger Information Hyperlinked over Proteins GFP-cDNA GoPubMed
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