Description Usage Arguments Details Value Author(s) References See Also Examples
KEGG Database API - Get the nucleotide acid and amino acid sequences
1 2 3 | getKEGGGeneSeq(KEGGGeneIDs, seqType = "aaseq", enforceURL = FALSE, n = 1)
doTen(tenWebSeq, seqType)
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KEGGGeneIDs |
A vector of KEGG IDs. Seqences from different species could be combined together. |
seqType |
Choose nucleotide acid (ntseq) or amino acid (aaseq) seqences, and the default is amino acid sequences. |
enforceURL |
whether to enfoce get get url until the results returned. The default value is "FALSE". |
n |
The number of CPUs or processors, and the default value is 1. |
tenWebSeq |
return results from function getURL() |
Get protein and gene sequences in fasta format. This function supports mutiple querys.
A BStringSet.
BStingSet or NULL (for the case one gene has no cording protein sequence)
Yulong Niu niuylscu@gmail.com
Yulong Niu niuylscu@gmail.com
http://www.kegg.jp/kegg/rest/keggapi.html
getKEGGTIDGeneSeq
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ## two amino acid seqences from different sepecies with 2 threads.
twoAASeqs <- getKEGGGeneSeq(c('mja:MJ_0011', 'hsa:10458'), n = 2)
## Not run:
## export fasta format files
require('Biostrings')
writeXStringSet(twoAASeqs, 'twoAASeqs.fasta')
## End(Not run)
## Not run:
## more examples
twoNTSeqs <- getKEGGGeneSeq(c('shy:SHJG_7159', 'shy:SHJG_7160'), 'ntseq')
mutilAASeqs <- getKEGGGeneSeq(c('eco:b0202', 'eco:b0203', 'eco:b0204',
'eco:b0205', 'eco:b0206', 'eco:b0216', 'eco:b0244',
'eco:b4626', 'eco:b3796', 'eco:b3797', 'eco:b3296',
'eco:b3297'))
## End(Not run)
## Not run:
## get the whole E.coli genome protein seqences
ecoProIDs <- getProID('eco')
ecoGenomePro <- getKEGGGeneSeq(ecoProIDs[, 1])
## End(Not run)
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