A tool for prediction of small RNA in RNA-Seq data

This diploma thesis focuses on the detection of small RNA (sRNA) in the bacterial genome. sRNAs are short non-coding transcripts that play a key role in gene expression. To date, there are several algorithms focusing on the detection of sRNAs from RNA-Sequencing (RNA-Seq) data that can be obtained by some of the sequencing platforms. The most frequently used platforms are Illumina and Ion Torrent belonging to the next generation sequencing and PacBio with Oxford Nanopore belonging to the third generation of sequencing. In this work, the workflow of sRNA detection using freely available tools was described and then an own unique tool for sRNA detection – the SEARCHsRNA tool – was designed. Two open-source software tools – Rockhopper and DETR'PROK, together with newly created tool, were tested on RNA-Seq data for bacteria Vibrio atlanticus LGP32