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comparison ITSx.xml @ 2:7c914d783d36 draft

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author okorol
date Tue, 24 Mar 2015 16:47:42 -0400
parents b433586432d7
children 02f17d884136
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1:b433586432d7 2:7c914d783d36
54 </tests> 54 </tests>
55 55
56 <help> 56 <help>
57 **What it does** 57 **What it does**
58 58
59 Identifies ITS sequences and extracts the ITS regions 59 Identifies ITS sequences and extracts the ITS regions.
60 60
61 ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. 61 ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.
62 62
63 ------ 63 ------
64 64
65 65
66 **Info** 66 **Galaxy wrapper**
67
68 Galaxy wrapper:
69 67
70 Microbial Biodiversity Bioinformatics Group 68 Microbial Biodiversity Bioinformatics Group
71 Agriculture and Agri-Food Canada 69 Agriculture and Agri-Food Canada
72 70
73 Contact: Oksana Korol, oksana.korol[at]agr.gc.ca 71 Contact: Oksana Korol, oksana.korol[at]agr.gc.ca
74 mbb[at]agr.gc.ca 72 mbb[at]agr.gc.ca
75 73
74 **ITSx tool**
75 Version: 1.0.11
76 Source code available at:http://microbiology.se/software/itsx
77 Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.
76 78
77 ITSx tool:
78
79 Version: 1.0.11
80 Source code available at:
81 http://microbiology.se/software/itsx
82
83 Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.
84 Contact: Johan Bengtsson-Palme, johan[at]microbiology.se 79 Contact: Johan Bengtsson-Palme, johan[at]microbiology.se
85 Programmer: Johan Bengtsson-Palme
86 80
87 81
88 **Citation** 82 **Citation**
89 83
90 Bengtsson-Palme, Johan and Ryberg, Martin and Hartmann, Martin and Branco, Sara and Wang, Zheng and Godhe, Anna and De Wit, Pierre and Sánchez-García, Marisol and Ebersberger, Ingo and de Sousa, Filipe and Amend, Anthony and Jumpponen, Ari and Unterseher, Martin and Kristiansson, Erik and Abarenkov, Kessy and Bertrand, Yann J. K. and Sanli, Kemal and Eriksson, K. Martin and Vik, Unni and Veldre, Vilmar and Nilsson, R. Henrik. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4;10:914-919, 2013. 84 Bengtsson-Palme et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4;10:914-919, 2013.
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92 85
93 </help> 86 </help>
94 87
95 </tool> 88 </tool>