Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System

The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated...

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Autores principales: Blanchard, Adam M., Leigh, James A., Egan, Sharon A., Emes, Richard D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Genetics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391243/
https://www.ncbi.nlm.nih.gov/pubmed/25914720
http://dx.doi.org/10.3389/fgene.2015.00139
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author Blanchard, Adam M.
Leigh, James A.
Egan, Sharon A.
Emes, Richard D.
author_facet Blanchard, Adam M.
Leigh, James A.
Egan, Sharon A.
Emes, Richard D.
author_sort Blanchard, Adam M.
collection PubMed
description The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS
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spelling pubmed-43912432015-04-24 Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System Blanchard, Adam M. Leigh, James A. Egan, Sharon A. Emes, Richard D. Front Genet Genetics The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS Frontiers Media S.A. 2015-04-09 /pmc/articles/PMC4391243/ /pubmed/25914720 http://dx.doi.org/10.3389/fgene.2015.00139 Text en Copyright © 2015 Blanchard, Leigh, Egan and Emes. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Blanchard, Adam M.
Leigh, James A.
Egan, Sharon A.
Emes, Richard D.
Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title_full Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title_fullStr Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title_full_unstemmed Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title_short Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System
title_sort transposon insertion mapping with pimms – pragmatic insertional mutation mapping system
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391243/
https://www.ncbi.nlm.nih.gov/pubmed/25914720
http://dx.doi.org/10.3389/fgene.2015.00139
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