DANSR : A Tool for the Detection of Annotated and Novel Small RNAs

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, snoR...

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Published inNon-coding RNA Vol. 8; no. 1; p. 9
Main Authors Zhang, Jin, Eteleeb, Abdallah M, Rozycki, Emily B, Inkman, Matthew J, Ly, Amy, Scharf, Russell E, Jayachandran, Kay, Krasnick, Bradley A, Mazur, Thomas, White, Nicole M, Fields, Ryan C, Maher, Christopher A
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 13.01.2022
MDPI
Subjects
Annotations
bioinformatics software
Cancer
Colon
colorectal cancer
Colorectal carcinoma
Decision trees
Gene expression
Genomes
Liver
Metastases
MicroRNAs
miRNA
next generation sequencing
Nucleotides
Proteins
small noncoding RNA
Transfer RNA
colorectal cancer
small noncoding RNA
next generation sequencing
bioinformatics software
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Summary: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.
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These authors contributed equally to this work.
ISSN:2311-553X
2311-553X
DOI:10.3390/ncrna8010009