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author proteore
date Fri, 28 Jun 2019 05:05:58 -0400
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1:f10816a9dd0b 2:1dea4e5f638f
1 <tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.02.21"> 1 <tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.06.27">
2 <description>[UniProt] 2 <description>[UniProt]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 5 <requirement type="package" version="3.4.1">R</requirement>
6 </requirements> 6 </requirements>
103 103
104 <help><![CDATA[ 104 <help><![CDATA[
105 105
106 **Description** 106 **Description**
107 107
108 This tool retrieves annotation (protein features) from the UniProt database (Mouse proteins) to enrich your protein IDs list. 108 This tool retrieves annotation (protein features) from the UniProt database (Mouse reference proteome) to enrich your protein IDs list.
109 109
110 ----- 110 -----
111 111
112 **Input** 112 **Input**
113 113
114 A list of Uniprot Accession Number (e.g. P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number**. If your input file contains other type of IDs, please use the ID_Converter tool. 114 A list of UniProt Accession Number (e.g. P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number**. If your input file contains other type of IDs, please use the ID_Converter tool.
115
116 .. class:: warningmark
117
118 In copy/paste mode, the number of UniProt AccNumber considered in input, is limited to 5000.
115 119
116 ----- 120 -----
117 121
118 **Parameters** 122 **Parameters**
119 123
120 "Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. 124 "Select features": Select each feature according to your interest by clicking the corresponding checkbox.
121 125
122 You can get more information about annotations `here <https://www.uniprot.org/help/uniprotkb_column_names>`_. 126 for more information about these features click `here <https://www.uniprot.org/help/uniprotkb_column_names>`_.
123 127
124 128
125 ----- 129 -----
126 130
127 **Output** 131 **Output**
131 135
132 ----- 136 -----
133 137
134 **Data source (release date)** 138 **Data source (release date)**
135 139
136 Annotations have been retrieved from UniProt.org (02/2019). 140 Annotations have been retrieved from UniProt.org (release 02/2019).
137 141
138 ----- 142 -----
139 143
140 .. class:: infomark 144 .. class:: infomark
141 145
142 **Authors** 146 **Authors**
143 147
144 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 148 David Christiany, Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
145 149
146 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 150 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
147 151
148 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 152 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
149 153
150 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 154 Help: contact@proteore.org for any questions or concerns about this tool.
151 155
152 ]]></help> 156 ]]></help>
153 <citations> 157 <citations>
154 </citations> 158 </citations>
155 159