Journal of Applied Bioinformatics & Computational BiologyISSN: 2329-9533

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Research Article, J Appl Bioinform Comput Biol Vol: 4 Issue: 2

EMOTE-conv: A Computational Pipeline to Convert Exact Mapping of Transcriptome Ends (EMOTE) Data to the Lists of Quantified Genomic Positions Correlated to Related Genomic Information

Haleh Yasrebi1,2* and Peter Redder1
1Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
2Swiss Institute of Bioinformatics, University of Geneva, Rue Michel-Servet 1,1211 Geneva 4, Switzerland
Corresponding author : Haleh Yasrebi
Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
E-mail: [email protected]
Received: August 12, 2015 Accepted: September 01, 2015 Published: September 07, 2015
Citation: Yasrebi H, Redder P (2015) EMOTE-conv: A Computational Pipeline to Convert Exact Mapping of Transcriptome Ends (EMOTE) Data to the Lists of Quantified Genomic Positions Correlated to Related Genomic Information. J Appl Bioinform Comput Biol 4:2 doi:10.4172/2329-9533.1000118

Abstract

EMOTE-conv: A Computational Pipeline to Convert Exact Mapping of Transcriptome Ends (EMOTE) Data to the Lists of Quantified Genomic Positions Correlated to Related Genomic Information

The determination of 5’-ends of RNA molecules is important for understanding various steps of gene expression and regulation in all organisms, such as transcription initiation, RNA maturation, and degradation. While previous methods like Phosphorylation Assay. By Ligation of Oligonucleotides, Rapid Amplification of Cdna Ends, Capped Analysis of Gene expression, tag RNA-seq and differential RNA-seq have their own specifications and limitations, Exact Mapping Of Transcriptome Ends (EMOTE) assay has been designed to determine the 5’-ends of RNAs on a transcriptome-wide scale. EMOTE-conv exploits the raw sequence reads generated from the EMOTE assay which is, to the best of our knowledge, the only method that can map the exact RNA 5’-ends of of all types on a transcriptome wide scale. It converts EMOTE data into the quantified list of genomic positions that corresponds to the 5’-end of RNA, signifying 5’-base RNA and the other related genomic information. EMOTE-conv is platform-independent, user-friendly and easy-to-use. It can be used with the data generated from other sequencing platforms with a converter as well as the data generated from any organism, species or strains. The EMOTE-conv software is available at: http://sourceforge.net/projects/emoteconv

Keywords: Transcriptome; 5’-end RNA; Genome mapping; Genomic positions; Illumina FASTQ; EMOTE

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