Question: Using UniProt.ws to retrieve protein features
0
gravatar for Guest User
5.7 years ago by
Guest User12k
Guest User12k 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: [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 > -- Sent via the guest posting facility at bioconductor.org.
uniprot.ws • 1.7k views
ADD COMMENTlink written 5.7 years ago by Guest User12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 207 users visited in the last hour