Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis.
BACKGROUND
Recent, rapid growth in the quantity of available genomic data has generated many protein sequences that are not yet biochemically classified. Thus, the prediction of biochemical function based on structural motifs is an important task in post-genomic analysis. The InterPro databases are a major resource for protein function information. For optimal results, these databases should be searched at regular intervals, since they are frequently updated.


RESULTS
We describe here a new program JIPS (Java GUI for InterProScan), a tool for tracking and viewing results obtained from repeated InterProScan searches. JIPS stores matches (in a local database) obtained from InterProScan searches performed with multiple versions of the InterPro database and highlights hits that have been added since the last search of the InterPro database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures.


CONCLUSIONS
JIPS is an efficient tool for performing repeated InterProScans on large batches of protein sequences, tracking and viewing search results, and mining the collected data.
Syed
Aijazuddin
A
Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada. asyed@uvic.ca
Upton
Chris
C
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
D011506:Proteins