Entering edit mode
7.2 years ago
gofre
•
0
Which bank should I connect to, to get Mycobacterium leprae TN, NC_002677 ?
question from https://a-little-book-of-r-for-bioinformatics.readthedocs.io/en/latest/src/chapter1.html
Q2. What is the length in nucleotides of the genome sequence for the bacterium Mycobacterium leprae strain TN (accession NC_002677)?
the ncbi page is https://www.ncbi.nlm.nih.gov/nuccore/15826865/
but using seqinr query, i could not find the correct database to connect to, to download the sequence in R.
> leprosyQuery <- query('leprosy', 'AC=NC_002677')
Error in query("leprosy", "AC=NC_002677") :
invalid request:"unknown accession number at (^): \"AC
Tried the banks in
> choosebank()
[1] "genbank" "embl" "emblwgs" "swissprot" "ensembl" "hogenom" "hogenomdna" "hovergendna"
[9] "hovergen" "hogenom5" "hogenom5dna" "hogenom4" "hogenom4dna" "homolens" "homolensdna" "hobacnucl"
[17] "hobacprot" "phever2" "phever2dna" "refseq" "greviews" "bacterial" "archaeal" "protozoan"
[25] "ensprotists" "ensfungi" "ensmetazoa" "ensplants" "ensemblbacteria" "mito" "polymorphix" "emglib"
[33] "refseqViruses" "ribodb" "taxodb"