BioWAP service
 
 

News release:

Developers of BioWap and Wigid combine their forces to further improve mobile bioinformatics services.

- Wigid home page

24.05.2004

BioWAP is a bioinformatics service for portable devices (such as mobile phones) with WAP (Wireless Application Protocol) compliance.

BioWAP provides access to all the major bioinformatics databases and analysis programs.

BioWAP facilitates use of bioinformatics services practically anytime anywhere.


What is Bioinformatics?


Bioinformatics is a new multidisciplinary field of science that maintains, processes, and analyses biological and biomedical data with computers. Huge databases are utilized for data mining.

What is WAP?

WAP is de facto global standard for the presentation and wireless delivery of information to mobile terminals. WAP is availbale by all the major mobile phone manufacturers, at least for some their models. It can be said that WAP brings Internet to mobile phones. WAP is a standardized procedure developed by WAP forum.

What does BioWAP provide?

BioWAP is part of the mBIOINFO service suite for bioinformatics. BioWAP facilitates searching information from all the major nucleotide and protein sequence databases, as well as study structural information and mutation data related to immunodeficiencies.

With BioWAP it is possible to search for general properties of sequences, user-defined patterns and restriction enzyme recognition sites.

Pairwise sequence aligments use the Needleman-Wunsch algorithm.

Prosite motifs can be identified from protein sequences. Specific mutation information can be searched from immunodeficiency mutation databases. Macromolecular structural information can be studied from PDB for compounds, references, resolution and location of secondary structural elements.

Further, the Enzyme Commission nomenclature is provided.

 
 
DATABASES:

Sequences:
EMBL, GenBank, SwissProt, TrEMBL, PIR, dbEST

Mutations:
BLMbase, BTKbase, CYBAbase, CYBBbase, CD3Ebase, CD3Gbase, CD40Lbase, JAK3base, NCF1base, NCF2base, RAG1base, RAG2base, SH2D1Abase, ZAP70base

Structure:
PDB

Enzyme Commission (EC) nomenclature


Sequence analysis
SRS


Nucleotides
General properties
    - length
    - number of nucleotides References
Alignment
    - two sequences
    - identity
    - number of gaps
Pattern search
Restriction enzyme sites

Proteins
General properties
    - molecular weight
    - number of residues
    - charge
References
Patterns
Motifs (Prosite)
Alignment
    - two sequences
    - identity / similarity
    - number of gaps


Mutations
Search by
    - PIN
    - location

References
    Structure
    General properties
    References
    Secondary structure

Enzyme
Search by
    - number
    - name

 
 
BioWAP program

The system was implemented with the WML language, while the server programs are written on Perl.

How to reach BioWAP?

The BioWAP can be accessed with any WAP device. The service is freely accesible through our own WAP gateway with no service charge. You may want to use the local WAP gateways (see http://www.wapdrive.net/).

If you can not reach the BioWAP service through gateway of your service provider, we maintain two gateways. Instructions on setting up your WAP-device in order to use our gateways can be found: http://bioinf.uta.fi/biowap/gateway.html. It usually possible to set up some alternative gateways in the WAP-device.

How to use BioWAP?

BioWAP is designed easy to use, however user interfaces of WAP-devices may vary a lot also lack of free memory can prevent downloading of some pages. Detailed instructions how to use BioWAP: http://bioinf.uta.fi/biowap/index.html.

Who has developed BioWAP?

BioWAP system has been developed in collaboration between

Prof. Mauno Vihinen Institute of Medical Technology, University of Tampere, Finland
and Prof. Tapio Salakoski Department of Computer Science, University of Turku, Finland
Drs. Jorma Boberg Department of Computer Science, University of Turku, Finland
Pentti Riikonen Department of Computer Science, University of Turku, Finland


IMT Bioinformatics group is a multidisciplinary research team working on many central areas of bioinformatics including databases, genomics, structure prediction and molecular dynamics simulations.

IMT Bioinformatics group has had for long collaboration with TUCS Bioinformatics group, University of Turku.

   
 
 

Publications:
  • Riikonen P, Boberg J, Salakoski T, Vihinen M.
    Mobile access to biological databases on the Internet
    (2002) Trans Biomed Eng. 49 (12) : 1477-9. [ MEDLINE ]

  • Riikonen, P., Boberg, J., Salakoski, T. and Vihinen, M.
    BioWAP, mobile bioinformatics
    (2001) Bioinformatics 17, 855-856. [ MEDLINE ]
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