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comparison README.rst @ 7:59da262c572c draft

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planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty
author proteore
date Mon, 28 May 2018 05:35:49 -0400
parents 72860740f65f
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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). 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 17
18 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. 18 After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to.
19 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. Please, note that a "NA" is returned when there is no corresponding ID. 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 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. 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 23
24 **Available databases** 24 **Available databases**
25 25
29 29
30 * Uniprot ID (e.g 1433B_HUMAN) 30 * Uniprot ID (e.g 1433B_HUMAN)
31 31
32 * Entrez gene ID (e.g. 7529) 32 * Entrez gene ID (e.g. 7529)
33 33
34 * RefSeq (NCBI) protein (e.g. NP_003395.1) 34 * RefSeq (NCBI) protein (e.g. NP_003395.1; NP_647539.1; XP_016883528.1)
35 35
36 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448) 36 * GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448; 377656701; 67464627; 78101741)
37 37
38 * Protein DataBank ID (e.g. 2BR9:A) 38 * Protein DataBank ID (e.g. 2BR9:A; 3UAL:A; 3UBW:A)
39 39
40 * GOterms (Gene Ontology) ID (e.g. GO:0070062) 40 * GOterms (Gene Ontology) ID (e.g. GO:0070062; GO:0005925; GO:0042470; GO:0016020; GO:0005739; GO:0005634)
41 41
42 * Protein Information Resource ID (e.g. S34755) 42 * Protein Information Resource ID (e.g. S34755)
43 43
44 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289) 44 * OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)
45 45
46 * Unigene ID (e.g. Hs.643544) 46 * Unigene ID (e.g. Hs.643544)
47 47
48 * Ensembl gene ID (e.g. ENSG00000166913) 48 * Ensembl gene ID (e.g. ENSG00000166913)
49 49
50 * Ensembl transcript ID (e.g. ENST00000353703) 50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839)
51 51
52 * Ensembl protein ID (e.g. ENSP00000300161) 52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930)
53 53
54 ----- 54 This tool converts human IDs using file built from:
55 55
56 .. class:: infomark 56 * HUMAN_9606_idmapping_selected.tab
57
58 This tool converts human IDs using the following source files:
59
60 * HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
61 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 57 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
62 58
63 * nextprot_ac_list_all.txt (Nextprot released on 01/08/2017) 59 * nextprot_ac_list_all.txt
64 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ 60 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
65
66 -----
67
68 .. class:: warningmark
69
70 Accession numbers with an hyphen ("-") that normally correspond to isoform are considered
71 (and will therefore be treated) as similar to its canonical form.
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73 For example, "Q71U36-2" will be treated as "Q71U36".