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Last seen 10.3 years ago
Hello,
I have just downloaded Bioconductor (v2.13) and the UniProt.ws (2.0.1)
packages. I want to retrieve all the feature information from a
protein, but when I search the column ???FEATURES??? I only get the
number of each type of feature, but not their whole lists. Is there
any way to get them?
Code example:
libraryUniProt.ws)
taxIdUniProt.ws) <- 9606
kt <- "UNIPROTKB"
keys <- c("Q9UNQ0") #Human BCRP
columns <- c("UNIPROTKB", "FEATURES")
res <- selectUniProt.ws, keys, columns, kt)
res
>UNIPROTKB
>1 Q9UNQ0
>FEATURES
>1 Alternative sequence (2); Chain (1); Disulfide bond (2); Domain
(2); Frameshift (2); Glycosylation (1); Mutagenesis (11); Natural
variant (18); Nucleotide binding (1); Sequence conflict (9); Site (2);
Topological domain (7); Transmembrane (6)
And I would like to have all the information for every one of those,
as we found them in UniProt
e.g. from http://www.uniprot.org/uniprot/Q9UNQ0.txt:
FT CHAIN 1 655 ATP-binding cassette sub-family G
member
FT 2.
FT /FTId=PRO_0000093386.
FT TOPO_DOM 1 395 Cytoplasmic (Potential).
FT TRANSMEM 396 416 Helical; (Potential).
FT TOPO_DOM 417 428 Extracellular (Potential).
FT TRANSMEM 429 449 Helical; (Potential).
[???]
I have already read the UniProt.ws documentation and searched for
older topics but I don???t find useful information.
Thank you in advance for any help.
David Gomez
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Mexico.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] UniProt.ws_2.2.0 RCurl_1.95-4.1 bitops_1.0-6 RSQLite_0.11.4
[5] DBI_0.2-7
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0
[4] IRanges_1.20.6 parallel_3.0.2 stats4_3.0.2
>
--
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