Mercurial > repos > proteore > proteore_get_unique_peptide_srm_method
comparison README.rst @ 0:a61b50b16a16 draft
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| author | proteore |
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| date | Wed, 10 Jul 2019 10:19:48 -0400 |
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| children | de6edb368dec |
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| 1 **Description** | |
| 2 | |
| 3 This tool allows you to get SRM/MRM informations from Uniprot-AC IDs. | |
| 4 | |
| 5 ----- | |
| 6 | |
| 7 **Input** | |
| 8 | |
| 9 A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing the wanted protein features. | |
| 10 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file. | |
| 11 | |
| 12 .. class:: warningmark | |
| 13 | |
| 14 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form. | |
| 15 | |
| 16 .. class:: warningmark | |
| 17 | |
| 18 In copy/paste mode, the number of IDs considered in input is limited to 5000. | |
| 19 | |
| 20 ----- | |
| 21 | |
| 22 **Parameters** | |
| 23 | |
| 24 - **Enter IDS:** enter your Uniprot-AC from a file or a copy paste | |
| 25 - **Release:** choose the release you want to use for retrieving protein sequences / features | |
| 26 - **Protein sequence/Features:** choose proteins features you want to retrieve | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **Output** | |
| 31 | |
| 32 A text file containing the selected protein features (in addition to the original column(s) provided). | |
| 33 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file. | |
| 34 | |
| 35 ----- | |
| 36 | |
| 37 **Data sources (release date)** | |
| 38 | |
| 39 This tool is using the following source file: | |
| 40 | |
| 41 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_. | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 .. class:: infomark | |
| 46 | |
| 47 **Authors** | |
| 48 | |
| 49 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
| 50 | |
| 51 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR | |
| 52 | |
| 53 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
| 54 | |
| 55 Help: contact@proteore.org for any questions or concerns about this tool. |