Ranked choice voting for representative transcripts with TRaCE
Abstract Summary Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical t...
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Published in | Bioinformatics Vol. 38; no. 1; pp. 261 - 264 |
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Main Authors | , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
22.12.2021
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Subjects | |
Online Access | Get full text |
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Summary: | Abstract
Summary
Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, Transcript Ranking and Canonical Election (TRaCE) holds an ‘election’ in which a set of RNA-seq samples rank transcripts by annotation edit distance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts.
Availability and implementation
Transcript ranking code can be found on GitHub at {{https://github.com/warelab/TRaCE}}.
Supplementary information
Supplementary data are available at Bioinformatics online. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1367-4803 1367-4811 1460-2059 1367-4811 |
DOI: | 10.1093/bioinformatics/btab542 |