[BioC] Howto annotate blast subject.id with AnnotationDbi

[Marc Carlson]

Hi Arnaud,

It should be fine as long as you remember that the shortened name is 
that of the locus ID, and that you are therefore annotating at the gene 
level (as is the case for all the org packages).

You can see the TAIR website for more clarification about what the 
different IDs mean.  Here is a page for the locus ID "AT1G01010":

http://www.arabidopsis.org/servlets/TairObject?type=locus&id=137158

And here is a page for the gene model "AT1G01010.1":

http://www.arabidopsis.org/servlets/TairObject?type=gene&id=138508


   Marc





On 05/27/2013 01:12 AM, Arnaud Mounier wrote:
> Hi,
>
> I try to annotate a blastp result (not so much, just 270 query) with 
> the org.At.tair.db from AnnotationDBi package throw bioconductor.
>
> First I read blast output with RFLPtools :
>
> > df.blast.report <- read.blast(file = f.blast.report)
> > head(df.blast.report)
>          query.id  subject.id identity alignment.length mismatches 
> gap.opens q.start q.end s.start s.end evalue bit.score
> 1 medtr8g018420.1 AT1G55020.1    59.77              860        314    
> 9       9   856      20   859      0      1058
> 2 medtr8g018420.1 AT3G22400.1    56.16              869        344   
> 10       9   856      34   886      0      1004
> 3 medtr8g018420.1 AT1G72520.1    45.19              821        433   
> 10      45   856     114   926      0       729
>
> The subject ID have version number (.1 or .2) and the original 
> ATH_GO_GOSLIM.txt from tair site two. But this version number is not 
> present in the org.At.tait.dbTAIR :
> > head(keys(org.At.tair.db, keytype="TAIR"))
> [1] "AT1G01010" "AT1G01020" "AT1G01030" "AT1G01040" "AT1G01050" 
> "AT1G01060"
>
>
> * Is this relevant or can I annotate without taking care of the 
> version number ?
> Does Org.At.tair.db keep the version number elsewhere ?
> Because the source file for this package 
> (ftp://ftp.arabidopsis.org/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.txt) 
> store it initialy.
>
> * As the query must be selected in function of her subjects 
> annotations and GO.db, I want to merge all info (blast report, 
> org.At.tair.db + GO.db) in one db with a bioconductor package 
> (annotationForge perhaps).
> So, is there a package or a GNU script to manage this association 
> easily or do i wrote my own R scripts ?
>
> Any links are welcomes !
> Thank's in advance,
> Ar.
>