Mercurial > repos > proteore > proteore_id_converter
diff README.rst @ 1:3b654cb3f6ad draft
planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
author | proteore |
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date | Tue, 27 Feb 2018 08:42:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Feb 27 08:42:18 2018 -0500 @@ -0,0 +1,60 @@ +Wrapper for ID Converter tool +============================= + +**Authors** + +T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +============================= + +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). + +After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. + +If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. + +If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file. + +**Available databases** + +* neXtProt ID (e.g. NX_P31946) + +* Uniprot accession number (e.g. P31946) + +* Uniprot ID (e.g 1433B_HUMAN) + +* Entrez gene ID (e.g. 7529) + +* RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1) + +* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741) + +* Protein DataBank ID (e.g. 2BR9:A; 3UAL:A; 3UBW:A) + +* GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634) + +* Protein Information Resource ID (e.g. S34755) + +* OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289) + +* Unigene ID (e.g. Hs.643544) + +* Ensembl gene ID (e.g. ENSG00000166913) + +* Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839) + +* Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930) + +This tool converts human IDs using file built from: + +* HUMAN_9606_idmapping_selected.tab + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* nextprot_ac_list_all.txt + Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ \ No newline at end of file