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ACTG: novel peptide mapping onto gene models

Title
ACTG: novel peptide mapping onto gene models
Author
백은옥
Keywords
RNA-SEQ; DATABASE
Issue Date
2017-04
Publisher
OXFORD UNIV PRESS
Citation
BIOINFORMATICS, v. 33, no. 8, page. 1218-1220
Abstract
In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model. Mapping potentially novel peptides to genome sequences, while allowing certain genomic variations, requires introducing novel gene models when aligning peptide sequences to gene structures. We have developed a new tool called ACTG (Amino aCids To Genome), which maps peptides to genome, assuming all possible single exon skipping, junction variation allowing three edit distances from the original splice sites, exon extension and frame shift. In addition, it can also consider SNVs (single nucleotide variations) during mapping phase if a user provides the VCF (variant call format) file as an input.
URI
https://academic.oup.com/bioinformatics/article/33/8/1218/2748210https://repository.hanyang.ac.kr/handle/20.500.11754/113693
ISSN
1367-4803; 1460-2059
DOI
10.1093/bioinformatics/btw787
Appears in Collections:
COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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