HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.
Bioinformatics
; 34(4): 675-677, 2018 02 15.
Article
in En
| MEDLINE
| ID: mdl-29444232
ABSTRACT
Summary:
Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications.Availability:
https//github.com/sahlenlab/HiCapTools. Contact pelinak@kth.se. Supplementary information Supplementary data are available at Bioinformatics online.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Chromosomes
/
Genomics
Type of study:
Diagnostic_studies
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2018
Document type:
Article
Affiliation country:
Sweden
Publication country:
ENGLAND
/
ESCOCIA
/
GB
/
GREAT BRITAIN
/
INGLATERRA
/
REINO UNIDO
/
SCOTLAND
/
UK
/
UNITED KINGDOM