Mercurial > repos > proteore > proteore_id_converter
comparison README.rst @ 1:3b654cb3f6ad draft
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| author | proteore |
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| date | Tue, 27 Feb 2018 08:42:18 -0500 |
| parents | |
| children | 72860740f65f |
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| 0:f2d0b13d9615 | 1:3b654cb3f6ad |
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| 1 Wrapper for ID Converter tool | |
| 2 ============================= | |
| 3 | |
| 4 **Authors** | |
| 5 | |
| 6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
| 7 | |
| 8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform | |
| 9 | |
| 10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
| 11 | |
| 12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. | |
| 13 | |
| 14 ============================= | |
| 15 | |
| 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). | |
| 17 | |
| 18 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. | |
| 19 | |
| 20 If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. | |
| 21 | |
| 22 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file. | |
| 23 | |
| 24 **Available databases** | |
| 25 | |
| 26 * neXtProt ID (e.g. NX_P31946) | |
| 27 | |
| 28 * Uniprot accession number (e.g. P31946) | |
| 29 | |
| 30 * Uniprot ID (e.g 1433B_HUMAN) | |
| 31 | |
| 32 * Entrez gene ID (e.g. 7529) | |
| 33 | |
| 34 * RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1) | |
| 35 | |
| 36 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741) | |
| 37 | |
| 38 * Protein DataBank ID (e.g. 2BR9:A; 3UAL:A; 3UBW:A) | |
| 39 | |
| 40 * GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634) | |
| 41 | |
| 42 * Protein Information Resource ID (e.g. S34755) | |
| 43 | |
| 44 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289) | |
| 45 | |
| 46 * Unigene ID (e.g. Hs.643544) | |
| 47 | |
| 48 * Ensembl gene ID (e.g. ENSG00000166913) | |
| 49 | |
| 50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839) | |
| 51 | |
| 52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930) | |
| 53 | |
| 54 This tool converts human IDs using file built from: | |
| 55 | |
| 56 * HUMAN_9606_idmapping_selected.tab | |
| 57 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ | |
| 58 | |
| 59 * nextprot_ac_list_all.txt | |
| 60 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ |