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Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 20 Nov 2015Publisher:Zenodo
Authors: Batzel, Peter; Desvignes, Thomas; Sydes, Jason; Eames, Brian F; Postlethwait, John H;
Code repository: https://github.com/uoregon-postlethwait/prost/tree/v0.7.34

doi: 10.5281/zenodo.35422 , 10.5281/zenodo.2588115 , 10.5281/zenodo.35418 , 10.5281/zenodo.34071 , 10.5281/zenodo.35461

Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis

Abstract

Prost! (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in chordates and vertebrates with assembled genomes. Prost! works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then “binned” together based on genomic location. Each bin is then annotated with miRBase mature sequences and hairpins, as well as other types of RNA obtained from Ensembl’s Biomart.

Related Organizations
Keywords

gene annotation, mirror-miRNA, seed-shifting, microRNA, isomiRs, miRNA families, miR-ome, miRNA editing, arm switching, seed, differential expression, miRNA

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    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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visibility
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
1
Average
Average
Average
35
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