Question: Using UniProt.ws to retrieve protein features
5.7 years ago by
Guest User • 12k
Guest User • 12k wrote:
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:  LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252  LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C  LC_TIME=Spanish_Mexico.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  UniProt.ws_2.2.0 RCurl_1.95-4.1 bitops_1.0-6 RSQLite_0.11.4  DBI_0.2-7 loaded via a namespace (and not attached):  AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0  IRanges_1.20.6 parallel_3.0.2 stats4_3.0.2 > -- Sent via the guest posting facility at bioconductor.org.
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