Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool

Cited 6 time in scopus
Metadata Downloads
Title
Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool
Author(s)
Jihyeob Mun; Dong Uk Kim; K L Hoe; Seon-Young Kim
Bibliographic Citation
BMC Bioinformatics, vol. 17, no. 17S, pp. 475-475
Publication Year
2016
Abstract
Background: Pooled library screen analysis using shRNAs or CRISPR-Cas9 hold great promise to genome-wide functional studies. While pooled library screens are effective tools, erroneous barcodes can potentially be generated during the production of many barcodes. However, no current tools can distinguish erroneous barcodes from PCR or sequencing errors in a data preprocessing step. Results: We developed the Barcas program, a specialized program for the mapping and analysis of multiplexed barcode sequencing (barcode-seq) data. For fast and efficient mapping, Barcas uses a trie data structure based imperfect matching algorithm which generates precise mapping results containing mismatches, shifts, insertions and deletions (indel) in a flexible manner. Barcas provides three functions for quality control (QC) of a barcode library and distinguishes erroneous barcodes from PCR or sequencing errors. It also provides useful functions for data analysis and visualization. Conclusions: Barcas is an all-in-one package providing useful functions including mapping, data QC, library QC, statistical analysis and visualization in genome-wide pooled screens.
Keyword
Barcode sequencingBarcoded yeast deletion strainsPooled library screen analysisSgRNAShRNATrie data structure based imperfect matching algorithm
ISSN
1471-2105
Publisher
Springer-BMC
DOI
http://dx.doi.org/10.1186/s12859-016-1326-9
Type
Article
Appears in Collections:
Division of Biomedical Research > Rare Disease Research Center > 1. Journal Articles
Korea Bioinformation Center > 1. Journal Articles
Files in This Item:

Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.