Sequence-based searching of custom proteome and transcriptome databases

Physiological Reports
Barbara MedvarTrairak Pisitkun

Abstract

A long-term goal in renal physiology is to understand the mechanisms involved in collecting duct function and regulation at a cellular and molecular level. The first step in modeling of these mechanisms, which can provide a guide to experimentation, is the generation of a list of model components. We have curated a list of proteins expressed in the rat renal inner medullary collecting duct (IMCD) from proteomic data from 18 different publications. The database has been posted as a public resource at https://hpcwebapps.cit.nih.gov/ESBL/Database/IMCD_Proteome_Database/. It includes 8956 different proteins. To search the IMCD Proteomic Database efficiently, we have created a Java-based program called curated database Basic Local Alignment Search Tool (cdbBLAST), which uses the NCBI BLAST kernel to search for specific amino acid sequences corresponding to proteins in the database. cdbBLAST reports information on the matched protein and identifies proteins in the database that have similar sequences. We have also adapted cdbBLAST to interrogate our previously published IMCD Transcriptome Database. We have made the cdbBLAST program available for use either as a web application or a downloadable .jar file at https://hpcwebapps.cit.nih...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 11, 2003·American Journal of Physiology. Renal Physiology·Jason D HoffertMark A Knepper
Oct 9, 2003·American Journal of Physiology. Renal Physiology·Bas W M van BalkomMark A Knepper
May 21, 2005·Molecular & Cellular Proteomics : MCP·Maria BarileMark A Knepper
Aug 5, 2005·Journal of the American Society of Nephrology : JASN·Ewout J HoornMark A Knepper
Feb 2, 2006·Physiological Genomics·Trairak PisitkunMark A Knepper
Apr 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jason D HoffertMark A Knepper
Aug 11, 2006·Molecular & Cellular Proteomics : MCP·Ming-Jiun YuMark A Knepper
Oct 25, 2007·Physiological Genomics·Panapat UawithyaMark A Knepper
Oct 17, 2008·American Journal of Physiology. Renal Physiology·Aaron N SachsMark A Knepper
Dec 10, 2009·Physiological Genomics·Dmitry TchapyjnikovMark A Knepper
Jan 16, 2010·Journal of the American Society of Nephrology : JASN·Amar D BansalMark A Knepper
Nov 24, 2011·Molecular & Cellular Proteomics : MCP·Jason D HoffertMark A Knepper
Nov 22, 2013·American Journal of Physiology. Renal Physiology·Jason D HoffertMark A Knepper
Mar 7, 2014·American Journal of Physiology. Cell Physiology·Davis BradfordTrairak Pisitkun
May 3, 2014·Kidney International·Francesco TrepiccioneBirgitte M Christensen
Mar 31, 2015·Journal of the American Society of Nephrology : JASN·Jae Wook LeeMark A Knepper
Oct 29, 2015·Physiological Genomics·Christina M PickeringMark A Knepper
May 21, 2016·Physiological Genomics·Barbara MedvarMark A Knepper
Oct 28, 2016·American Journal of Physiology. Renal Physiology·Sophia M LeMaireMark A Knepper

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Software Mentioned

makeblastdb
Notepad
NetBeans IDE
Nedd4l
cdbBLAST
BLAST
Automated Bioinformatics Extractor ( ABE )
blastp
Affymetrix
Excel

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