r - Genbank query (package seqinr): searching in sequence description -


i using function query() of package seqinr download myoglobin dna sequences genbank. e.g.:

query("myoglobins","k=myoglobin , sp=turdus merula") 

unfortunately, lot of species i'm looking don't sequence @ (or species, short one), though find sequences when search manually on website. because of searching "myoglobin" in keywords only, while there isn't entry in there. protein type specified in name ("definition" on genbank) -- have no idea how search this. page on query() doesn't seem offer option in details, "generic search" without "k=" doesn't work, , haven't found via googling.

i'd happy links, explanations , help. thank you! :)

there complete manual seqinr package describes query language more in depth in chapter 5 (available @ http://seqinr.r-forge.r-project.org/seqinr_2_0-1.pdf). trying similar query , description many of genes/cds blank don't come when searching using k= option. 1 alternative search organism alone, match gene names in individual annotations , pull out accession numbers, use re-query database sequences.

this pull out annotation first gene:

choosebank("embltp")  query("acexample", "sp=turdus merula")  getname(acexample$req[[1]])  annotations <- getannot(acexample$req[[1]])  cat(annotations, sep = "\n") 

i think pretty time consuming way tackle problem there doesn't seem efficient way of searching annotations directly. i'd interested in solutions might come with.


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