"The price of greatness is responsibility." Sir Winston Churchill

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The Bioinformativ-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 special ranking systems similar to Google pagerank sorts the search results and displays most relevant information.

Contents [hide] 1 How does Harvester work? 2 What can i find? 3 How to link your project or excel-sheet to the Bioinformatic Harvester 4 Weblinks

 

How does Harvester work?

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 ~72.000 human (2005-08) ~48.000 mouse and ~15.000 rat protein information pages which are curated and updated on a regular basis.

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, proteins 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 realtime view on 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

 

What can i find?

Harvester allows both 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 "diseaslink"
• Combinations: "golgi diseaselink" (finds all golgi proteins associated with a disease)
• mRNA: "AL136897"

• Word: "Cancer"
• Comment: "highly expressed in heart"
• Author: "Bush, Schroeder"
• Publication oder project: "cDNA sequencing project"

 

How to link your project or excel-sheet to the Bioinformatic Harvester

The following query string searches the human set of proteins. Simply replace the term "brain" with your search term.

http://www-db.embl.de/jss/servlet/de.embl.bk.htmlfind.HarvesterOutputMysql?m=doSearch&fH=0&search=brain

• Use &fH=0 for searches within the human protein set
• Use &fH=1 for searches within the mouse protein set
• Use &fH=2 for searches within the rat protein set

 

 

Weblinks

• http://harvester.embl.de