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SEMESTER PROJECT PRESENTATION

SEMESTER PROJECT PRESENTATION. CS 6030 – Bioinformatics Instructor Dr.Elise de Doncker Chandana Guduru Jason Eric Johnson. INTRODUCTION.

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SEMESTER PROJECT PRESENTATION

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  1. SEMESTER PROJECT PRESENTATION CS 6030 – Bioinformatics Instructor Dr.Elise de Doncker Chandana Guduru Jason Eric Johnson

  2. INTRODUCTION • Our project will consist of a mobile application for iPad that will allow a user to make use of various web APIs available from the European Biometrics Institute1 (EBI). • The EBI provides a large number of functions in the areas of Data Retrieval, Analysis Tools, Sequence Similarity Search2, Multiple Sequence Alignment3, Phylogeny4, Pairwise Sequence Analysis5, Sequence Statistics6, Sequence Translations7, Structural Analysis8 and Literature and Ontology database searches

  3. GOALS • Allows the user to create the jobs by selection. • It also allows the user to input to appropriate parameters. • To implement the jobs through the EBI APIs.

  4. POSSIBLE APPROACHES • To choose specific functions that are feasible at any given time. • Application should be used for several types of query.

  5. NCBI BLAST (REST) • Uses two programmatic methods to submit BLAST searches. • RESTful INTERFACE: REST stands for Representational State Transfer. In RESTful Interface each unique URL is a representation of some object SOAP INTERFACE: SOAP stands for Simple Object Access Protocol.It is used for specification for exchanging structured information in the implementation of Web Services.  It relies on Extensible Markup Language (XML) for its message format

  6. Ncbi blast • Sequence similarity search program. • To find regions of sequence similarity which will yield functional and evolutionary clues. • WU-BLAST10 and NCBI BLAST do their work differently to obtain different results

  7. RESTFUL INTERFACE • Allows submission of BLAST searches for processing at NCBI via an HTTP-based interface. • The normal BLAST report is a human readable output which may change with a little or no notice.

  8. ADVANTAGES OF USING HTTP REQUESTS • No program should be downloaded from NCBI ftp site to use NCBI BLAST service. • Easy to keep backward compatibility of API. • No need to transfer sequences from NCBI to local machines. • No need to hack Web NCBI BLAST programs to run scripts.

  9. FUTURE ENHANCEMENTS • Implement other available search types soon. • Offer for free of cost on the iTunes App store hosting it on GitHub. • Implementation of any search through a web API from the EBI. • Allowing the deletion of previous jobs, personalization of requests and user authorization. • Allow the export of results in various formats to other applications.

  10. IMPLEMENTATION • Master/Detail Application • Implemented in objective C using the Xcode IDE and Cocoa Touch framework. • Easy way of selection and entry of information for the searches. • Allows for selection from a master list of services than the application provides.

  11. testing • Several sets of test data9 from the University of Texas Health Science Center, San Antonio have been used. • Searches can be run through the web interface at the NCBI.

  12. REFERENCES 1) http://www.ebi.ac.uk/2) http://www.ebi.ac.uk/Tools/sss/3) http://www.ebi.ac.uk/Tools/msa/4) http://www.ebi.ac.uk/Tools/phylogeny/5) http://www.ebi.ac.uk/Tools/psa/6) http://www.ebi.ac.uk/Tools/seqstats/7) http://www.ebi.ac.uk/Tools/st/8) http://www.ebi.ac.uk/Tools/structural.html9)http://biochem.uthscsa.edu/~hs_lab/tech/testseqs.html 10) http://www.uthscsa.edu 11) http://www.petefreitag.com/item/431.cfm

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