TY - JOUR
T1 - DANSR
T2 - A Tool for the Detection of Annotated and Novel Small RNAs
AU - Zhang, Jin
AU - Eteleeb, Abdallah M.
AU - Rozycki, Emily B.
AU - Inkman, Matthew J.
AU - Ly, Amy
AU - Scharf, Russell E.
AU - Jayachandran, Kay
AU - Krasnick, Bradley A.
AU - Mazur, Thomas
AU - White, Nicole M.
AU - Fields, Ryan C.
AU - Maher, Christopher A.
N1 - Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/2
Y1 - 2022/2
N2 - Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.
AB - Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.
KW - Bioinformatics software
KW - Colorectal cancer
KW - Next generation sequencing
KW - Small noncoding RNA
UR - http://www.scopus.com/inward/record.url?scp=85123712351&partnerID=8YFLogxK
U2 - 10.3390/ncrna8010009
DO - 10.3390/ncrna8010009
M3 - Article
C2 - 35076605
AN - SCOPUS:85123712351
SN - 2311-553X
VL - 8
JO - Non-coding RNA
JF - Non-coding RNA
IS - 1
M1 - 9
ER -