Before starting
Over recent years, deep sequencing technology has become a powerful approach for deeply investigating small non-coding RNA (ncRNA) populations, i.e. small RNA-seq. It is now established that an increasing number of novel small ncRNA families distinct from microRNAs are generated over kingdoms from different coding/non-coding regions via various biogenesis pathways and might involve a great spectrum of biological processes. For example, two other major classes of endogenous small RNAs, Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs), have been identified and widely investigated in mammals [7]. Moreover, in other organisms like plants more classes of small ncRNA have been described indicating that a wide range of small ncRNAs exist [3].
However, most of the existing tools devoted to sRNA-seq analysis, are only based on miRNAs annotation and quantification, or can only be applied to one organism. Here we present a comprehensive and flexible ncRNA analysis pipeline, ncPRO-seq (Non-Coding RNA PROfiling in sRNA-seq) (http://ncproseq.sourceforge.net), which is able to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase [8], Rfam [5] and repeatMasker [14], and regions defined by users. The ncPRO-seq pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that small RNA raw data from the 3 current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) could be analyzed with this pipeline. Finally, the ncPRO-seq pipeline can be used to analyze data based on genome from metazoan to plants.
Chongjian Chen
2012-01-26
