Description Usage Arguments Details Value Author(s) References See Also Examples
KEGG Database API - Get the nucleotide acid and amino acid sequences
1 | getKEGGGeneSeq(KEGGID, seqType = "aaseq", n = 4)
|
KEGGID |
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. |
n |
The number of CPUs or processors, and the default value is 4. |
Get the protein and gene sequences in fasta format. This function support mutiple querys.
A BStringSet
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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.