ArticlePhysiological reports2018
Sequence-based searching of custom proteome and transcriptome databases.
Article in Physiological reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed, 1 citations in OpenAlex.
- Sequence-based searching of custom proteome and transcriptome databases.Physiological reports · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.