Mercurial > repos > proteore > proteore_id_converter

annotate README.rst @ 2:f8564e97ccd9 draft

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date Fri, 24 Aug 2018 04:35:33 -0400
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1 Wrapper for ID Converter tool
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2 =============================
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4 **Authors**
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5
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6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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14 =============================
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16 This tool converts a list of IDs to another identifier type, select the source and target type from the dropdown menus above (see below supported source and target types).
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18 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to.
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20 If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs.
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22 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
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24 **Available databases**
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26 * neXtProt ID (e.g. NX_P31946)
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28 * Uniprot accession number (e.g. P31946)
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30 * Uniprot ID (e.g 1433B_HUMAN)
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32 * Entrez gene ID (e.g. 7529)
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34 * RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1)
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36 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741)
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38 * Protein DataBank ID (e.g. 2BR9:A; 3UAL:A; 3UBW:A)
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40 * GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634)
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42 * Protein Information Resource ID (e.g. S34755)
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44 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)
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46 * Unigene ID (e.g. Hs.643544)
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48 * Ensembl gene ID (e.g. ENSG00000166913)
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50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839)
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52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930)
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54 This tool converts human IDs using file built from:
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56 * HUMAN_9606_idmapping_selected.tab
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57 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
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59 * nextprot_ac_list_all.txt
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60 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/