PITDB: a database of translated genomic elements

Shyamasree Saha, Eleni A. Chatzimichali, David A. Matthews, Conrad Bessant*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

1 Citation (Scopus)
220 Downloads (Pure)

Abstract

PITDB is a freely available database of translated genomic elements (TGEs) that have been observed in PIT (proteomics informed by transcriptomics) experiments. In PIT, a sample is analyzed using both RNAseq transcriptomics and proteomic mass spectrometry. Transcripts assembled from RNA-seq reads are used to create a library of sample-specific amino acid sequences against which the acquired mass spectra are searched, permitting detection of any TGE, not just those in canonical proteome databases. At the time of writing, PITDB contains over 74 000 distinct TGEs from four species, supported by more than 600 000 peptide spectrum matches. The database, accessible via http://pitdb.org, provides supporting evidence for each TGE, often from multiple experiments and an indication of the confidence in the TGE's observation and its type, ranging from known protein (exact match to a UniProt protein sequence), through multiple types of protein variant including various splice isoforms, to a putative novel molecule. PITDB's modern web interface allows TGEs to be viewed individually or by species or experiment, and downloaded for further analysis. PITDB is for bench scientists seeking to share their PIT results, for researchers investigating novel genome products in model organisms and for those wishing to construct proteomes for lesser studied species.

Original languageEnglish
Article numbergkx906
Pages (from-to)D1223-D1228
Number of pages6
JournalNucleic Acids Research
Volume46
Issue numberD1
Early online date9 Oct 2017
DOIs
Publication statusPublished - 4 Jan 2018

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