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Sequence-based searching of custom proteome and transcriptome databases.

Barbara Medvar1,2,3, Abhijit Sarkar1,2,3, Mark Knepper1

  • 1Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.

Physiological Reports
|September 20, 2018
PubMed
Summary
This summary is machine-generated.

Researchers created a database of 8956 proteins in the rat renal inner medullary collecting duct (IMCD). A new tool, cdbBLAST, enables efficient searching of this proteomic database by protein sequence.

Keywords:
BLASTIMCDdatabasekidney

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Area of Science:

  • Renal Physiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding renal collecting duct function requires detailed molecular and cellular knowledge.
  • Modeling these mechanisms necessitates comprehensive component lists.
  • Rat inner medullary collecting duct (IMCD) proteomic data from multiple studies were compiled.

Purpose of the Study:

  • To curate a comprehensive proteomic database of the rat IMCD.
  • To develop an efficient search tool for the IMCD proteomic database.
  • To facilitate the identification of functionally related proteins.

Main Methods:

  • Proteomic data from 18 publications were integrated to create the IMCD Proteome Database.
  • A Java-based program, curated database Basic Local Alignment Search Tool (cdbBLAST), was developed using the NCBI BLAST kernel.
  • cdbBLAST was adapted to search both the IMCD Proteome Database and the IMCD Transcriptome Database by amino acid sequence.

Main Results:

  • The IMCD Proteome Database contains 8956 unique proteins.
  • cdbBLAST enables efficient sequence-based searching of the database.
  • The tool identifies proteins with similar sequences, aiding in functional role identification.

Conclusions:

  • The curated IMCD Proteome Database and the cdbBLAST tool provide valuable resources for renal physiology research.
  • Sequence-based searching offers advantages over gene symbol searches by reducing ambiguity and identifying related proteins.
  • These resources will guide experimentation and enhance understanding of IMCD function.