Sequence-based searching of custom proteome and transcriptome databases.

Medvar, Barbara, Sarkar, Abhijit, Knepper, Mark and Pisitkun, Trairak ORCID: 0000-0001-6677-2271 (2018) Sequence-based searching of custom proteome and transcriptome databases. Physiological reports, 6 (18). e13846-.

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Official URL: http://dx.doi.org/10.14814/phy2.13846

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.gov/ESBL/Database/cdbBLAST/. Database searching based on protein sequence removes ambiguities arising from the standard search method based on official gene symbols and allows the user efficient identification of related proteins that may fulfill the same functional roles.

Item Type:	Article
Uncontrolled Keywords:	Kidney Medulla, Animals, Rats, Proteome, Amino Acid Sequence, Databases, Genetic, Transcriptome
Depositing User:	Symplectic Admin
Date Deposited:	21 Feb 2020 10:46
Last Modified:	19 Jan 2023 00:01
DOI:	10.14814/phy2.13846
Open Access URL:	https://doi.org/10.14814/phy2.13846
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3076020