Prost!

Prost! (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. Prost! does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single Prost! run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, Prost! then annotates them using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally Prost! contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the Prost! analysis is provided in an Excel output file so that the user have access to all information for deeper analysis of specific cases.

Documentation

For further information on Prost!, please see the full documentation at https://prost.readthedocs.org.

Authors

• Peter Batzel - Conceptual Design, Software Engineering, and Algorithm Design
• Thomas Desvignes - Conceptual Design Leader
• Jason Sydes - Conceptual Design, Software Engineering, and Algorithm Design
• Brian F. Eames - Prototype Design
• John H. Postlethwait - Project Advisor

Funding

Prost! has been funded by the following grants:

• Identification of MiRNAs Involving Midfacial Development and Clefting; NIH - National Institute of Dental and Craniofacial Research (U01 DE020076)
• Advancing the Scientific Potential of Transcriptomics in Aquatic Models; NIH - Office of the Director (R24 OD011199)
• Resources for Teleost Gene Duplicates and Human Disease; NIH - Office of the Director (R01 OD011116)
• Mechanisms of Sex Determination in Zebrafish; NIH - National Institute of General Medical Sciences (R01 GM085318)
• Developmental Mechanisms for the Evolution of Bone Loss; NIH - National Institute on Aging (R01 AG031922)
• Signaling Hierarchies in Vertebrate Development: CP1: A zebrafish model of phenotypic variation associated with Fraser syndrome; NIH - Eunice Kennedy Shriver National Institute of Child Health and Human Development (P01 HD22486)

Citing Prost!

If you use Prost!, please cite it like so:

Thomas Desvignes, Peter Batzel, Jason Sydes, B. Frank Eames, and John H. Postlethwait. 2019. “MiRNA Analysis with Prost! Reveals Evolutionary Conservation of Organ-Enriched Expression and Post-Transcriptional Modifications in Three-Spined Stickleback and Zebrafish.” Scientific Reports 9 (1): 3913. https://doi.org/10.1038/s41598-019-40361-8.

Prost! has been previously cited like so:

Thomas Desvignes, Peter Batzel, Jason Sydes, B. Frank Eames, & John H. Postlethwait. (2019, March 9). Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis (Version v0.7.53). Zenodo. http://doi.org/10.5281/zenodo.594353.