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HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications
KTH, Skolan för bioteknologi (BIO). KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
KTH, Skolan för bioteknologi (BIO). KTH, Centra, Science for Life Laboratory, SciLifeLab.
KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
2018 (Engelska)Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, nr 4, s. 675-677Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

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.

Ort, förlag, år, upplaga, sidor
OXFORD UNIV PRESS , 2018. Vol. 34, nr 4, s. 675-677
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
URN: urn:nbn:se:kth:diva-223786DOI: 10.1093/bioinformatics/btx625ISI: 000424889300018PubMedID: 29444232Scopus ID: 2-s2.0-85042539364OAI: oai:DiVA.org:kth-223786DiVA, id: diva2:1188301
Forskningsfinansiär
Vetenskapsrådet, 78081
Anmärkning

QC 20180307

Tillgänglig från: 2018-03-07 Skapad: 2018-03-07 Senast uppdaterad: 2018-03-07Bibliografiskt granskad

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Anil, AnandashankarSpalinskas, RapolasÅkerborg, ÖrjanSahlén, Pelin
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Skolan för bioteknologi (BIO)Science for Life Laboratory, SciLifeLab
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