UMMS Affiliation
Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2016-10-01
Document Type
Article
Disciplines
Bioinformatics | Computational Biology | Genomics | Integrative Biology
Abstract
With the rapid accumulation of publicly available small RNA sequencing datasets, third-party meta-analysis across many datasets is becoming increasingly powerful. Although removing the 3 adapter is an essential step for small RNA sequencing analysis, the adapter sequence information is not always available in the metadata. The information can be also erroneous even when it is available. In this study, we developed DNApi, a lightweight Python software package that predicts the 3 adapter sequence de novo and provides the user with cleansed small RNA sequences ready for down stream analysis. Tested on 539 publicly available small RNA libraries accompanied with 3 adapter sequences in their metadata, DNApi shows near-perfect accuracy (98.5%) with fast runtime (~2.85 seconds per library) and efficient memory usage (~43 MB on average). In addition to 3 adapter prediction, it is also important to classify whether the input small RNA libraries were already processed, i.e. the 3 adapters were removed. DNApi perfectly judged that given another batch of datasets, 192 publicly available processed libraries were "ready-to-map" small RNA sequence. DNApi is compatible with Python 2 and 3, and is available at https://github.com/jnktsj/DNApi. The 731 small RNA libraries used for DNApi evaluation were from human tissues and were carefully and manually collected. This study also provides readers with the curated datasets that can be integrated into their studies.
Keywords
small RNA sequencing datasets, 3´ adapter sequence, downstream analysis
DOI of Published Version
10.1371/journal.pone.0164228
Source
PLoS One. 2016 Oct 13;11(10):e0164228. doi: 10.1371/journal.pone.0164228. eCollection 2016. Link to article on publisher's site
Journal/Book/Conference Title
PloS one
Related Resources
PubMed ID
27736901
Repository Citation
Tsuji, Junko and Weng, Zhiping, "DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data" (2016). Program in Bioinformatics and Integrative Biology Publications and Presentations. 96.
https://escholarship.umassmed.edu/bioinformatics_pubs/96
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Bioinformatics Commons, Computational Biology Commons, Genomics Commons, Integrative Biology Commons