Automated family-based naming of small RNAs for next generation sequencing data using a modified MD5-digest algorithm

TL;DR

NameMyGene is a user-friendly tool that automatically assigns family-based names to small RNA sequences, facilitating organization and pattern recognition in large sequencing datasets without needing extra data.

Contribution

It introduces a novel web and standalone tool that uses a modified MD5-digest algorithm for naming small RNAs based solely on their sequences.

Findings

Enables easy organization of small RNA data

Applicable to RNA-Seq and ChIP-Seq data

Platform-independent Java implementation

Abstract

We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data generated by next-generation sequencers. NameMyGene, also applicable to other emerging methods such as RNA-Seq, and Chip-Seq, solely uses the input small RNA sequence and does not require any additional data such as other sequence data sets. The web server and software is freely available (http://www.johnlab.org/NameMyGene) and is based on Java to ensure platform independency.