SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes

Fiebig, M., Gluenz, E. , Carrington, M. and Kelly, S. (2014) SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Molecular and Biochemical Parasitology, 196(2), pp. 71-74. (doi: 10.1016/j.molbiopara.2014.07.012) (PMID:25111964) (PMCID:PMC4222701)

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Abstract

The Kinetoplastida are a diverse and globally distributed class of free-living and parasitic single-celled eukaryotes that collectively cause a significant burden on human health and welfare. In kinetoplastids individual genes do not have promoters, but rather all genes are arranged downstream of a small number of RNA polymerase II transcription initiation sites and are thus transcribed in polycistronic gene clusters. Production of individual mRNAs from this continuous transcript occurs co-transcriptionally by trans-splicing of a ∼39 nucleotide capped RNA and subsequent polyadenylation of the upstream mRNA. SLaP mapper (Spliced-Leader and Polyadenylation mapper) is a fully automated web-service for identification, quantitation and gene-assignment of both spliced-leader and polyadenylation addition sites in Kinetoplastid genomes. SLaP mapper only requires raw read data from paired-end Illumina RNAseq and performs all read processing, mapping, quality control, quantification, and analysis in a fully automated pipeline. To provide usage examples and estimates of the quantity of sequence data required we use RNAseq obtained from two different library preparations from both Trypanosoma brucei and Leishmania mexicana to show the number of expected reads that are obtained from each preparation type. SLaP mapper is an easy to use, platform independent webserver that is freely available for use at http://www.stevekellylab.com/software/slap. Example files are provided on the website.

Item Type:Articles
Additional Information:MF is supported by the Wellcome Trust. SK is a Leverhulme Trust Early Career Fellow. EG is a Royal Society University Research Fellow. MC is supported by the Wellcome trust 085256/Z/08/Z.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gluenz, Dr Eva
Authors: Fiebig, M., Gluenz, E., Carrington, M., and Kelly, S.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Molecular and Biochemical Parasitology
Publisher:Elsevier
ISSN:0166-6851
ISSN (Online):1872-9428
Published Online:08 August 2014
Copyright Holders:Copyright © 2014 The Authors
First Published:First published in Molecular and Biochemical Parasitology 196(2)71-74
Publisher Policy:Reproduced under a Creative Commons license

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