Interactive web-based identification and visualization of transcript shared sequences

Alaleh Azhir; Louis-Henri Merino; David W Nauen

doi:10.1016/j.ygeno.2018.05.010

Interactive web-based identification and visualization of transcript shared sequences

Genomics. 2019 Jul;111(4):860-862. doi: 10.1016/j.ygeno.2018.05.010. Epub 2018 May 12.

Authors

Alaleh Azhir¹, Louis-Henri Merino², David W Nauen³

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
² Department of Computer Science, University of Maryland - College Park, College Park, MD 20742, USA.
³ Department of Pathology, Johns Hopkins School of Medicine, Baltimore 21205, USA. Electronic address: dwnauen@jhmi.edu.

PMID: 29763731
DOI: 10.1016/j.ygeno.2018.05.010

Abstract

We have developed TraC (Transcript Consensus), a web-based tool for detecting and visualizing shared sequences among two or more mRNA transcripts such as splice variants. Results including exon-exon boundaries are returned in a highly intuitive, data-rich, interactive plot that permits users to explore the similarities and differences of multiple transcript sequences. The online tool (http://labs.pathology.jhu.edu/nauen/trac/) is free to use. The source code is freely available for download (https://github.com/nauenlab/TraC).

Keywords: Alternative splicing; RNA; Splice variant; Visualization.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Consensus Sequence*
Humans
RNA Splicing*
RNA, Messenger / chemistry
RNA, Messenger / genetics*
Sequence Analysis, RNA / methods*
Software*
Transcriptome

Substances

RNA, Messenger

Grants and funding

R25 NS079185/NINDS NIH HHS/National Institute of Neurological Disorders and Stroke/United States