Bioinformatic Harvester

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The Bioinformatic-Harvester is a bioinformatic meta search engine for genes and protein-associated information. Harvester currently works for human, mouse and rat proteins. Harvester crosslinks 16 popular bioinformatic resources and allows cross searches. A ranking system similar to Google pagerank sorts the search results and displays the more relevant information.

Databases supported by Bioinformatic Harvester

1 How Harvester works
2 What one can find
3 See also
4 Literature
5 External links

[edit] How Harvester works

Harvester collects information from protein and gene databases along with information from so called "prediction servers." Prediction server e.g provide online sequence analysis for a single protein. Harvesters search index is based on the UniProt protein information collection. The Uniprot collections consists of ~71.000 human (2006-04) ~62.000 mouse and ~15.000 rat protein information pages which are curated and updated on a regular basis.

A screenshot of the Harvester browser

Harvester collects two types of information:

A) text based information from the following databases:

UniProt, world largest protein database
SOURCE, convenient gene information overview
Simple Modular Architecture Research Tool (SMART),
SOSUI, predicts transmembrane domains
PSORT, predicts protein localisation
Homologene, compares proteins from different species
gfp-cdna, protein localisation with fluorescence microscopy
International Protein Index (IPI).

B) Databases rich in graphical elements are not collected, but crosslinked via iframes. Iframes are transparent windows within a HTML pages. The iframe windows allows up-to-date viewing of the "iframed," linked databases. Several such iframes are combined on a Harvester protein page. This mehtod allows convenient comparison of information from several databases.

Currently Harvester crosslinks the following (graphical elements rich) servers via iframes:

NCBI-BLAST, an algorithm for comparing biological sequences NCBI
Genome Browser, working draft assemblies for genomes UCSC
Ensembl, automatic gene annotation. EMBL-EBI and Sanger-Institute
RZPD, German resources Center for genome research in Berlin/Heidelberg
STRING, Search Tool for the Retrieval of Interacting Genes/Proteins EMBL
iHOP, information hyperlinked over proteins via gene/protein synonyms

[edit] What one can find

Harvester allows a combination of different search terms and single words.

Search Examples:

Gene-name: "golga3"
Gene-alias: "ADAP-S ADAS ADHAPS ADPS" (one gen name is sufficient)
Gene-Ontologies: "Enzyme linked receptor protein signaling pathway"
Unigene-Cluster: "Hs.449360"

Go-annotation: "intra-Golgi transport"
Molecular function: "protein kinase binding"
Protein: "Q9NPD3"
Protein domain: "SH2 sar"
Protein Localisation: "endoplasmic reticulum"

Chromosome: "2q31"
Disease relevant: use the word "diseaselink"
Combinations: "golgi diseaselink" (finds all golgi proteins associated with a disease)
mRNA: "AL136897"

Word: "Cancer"
Comment: "highly expressed in heart"
Author: "Merkel, Schmidt"
Publication or project: "cDNA sequencing project"

[edit] See also

[edit] Literature

Liebel,U., & Kindler,B.,Pepperkok,R. (2004) 'Harvester': a fast meta search engine of human protein resources. Bioinformatics. 2004 Aug 12;20(12):1962-3. Epub 2004 Feb 26.[1]

Liebel,U., & Kindler,B.,Pepperkok,R. (2004) Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources. Methods Enzymol. 2005;404:19-26[2]