How can I annotate multiple blast results?

Question

[Assa Yeroslaviz]

Hi, I have a list of hits from a magicblast run against a fastq file I have. I was wondering if there is a way to annotate the hits I get. The run was done against nt DB.

The list of hits looks like that:

NB500982:283:HH3WJAFX2:1:21210:15709:8224   gi|1040217674   100 0   0   0   1...
NB500982:283:HH3WJAFX2:1:21210:20062:8227   gi|1040160167   100 0   0   0   1...
NB500982:283:HH3WJAFX2:1:21210:4790:8228    gi|1040197389   100 0   0   0   1...
NB500982:283:HH3WJAFX2:1:21210:12133:8228   gi|164790   98.6667 0   0   0   1...

The gene ID is in the second column.

Thanks

Assa

[lieven.sterck]

what exactly do you mean with 'annotate'? like get the description line of each hit ?

[Assa Yeroslaviz]

Yes, I would like to get the gene name and organism.

[lieven.sterck]

after looking into the 'manual' of magicblast I don't think you can get that directly from the magicblast output.

You can however run all the hit IDs through entrez or such and retrieve the description for them.

[Assa Yeroslaviz]

I know I can't get it via magicblast. My question is how I can get it otherwise.

Answer 1

[GenoMax]

Using EntrezDirect:

$ more gi
1040217674
1040160167
1040197389

$ for i in `cat gi`; do printf ${i}"\t"; esearch -db nuccore -query ${i} | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description,ScientificName; done
1040217674  PROKR2  prokineticin receptor 2 Oryctolagus cuniculus
1040160167  CCDC180 coiled-coil domain containing 180   Oryctolagus cuniculus
1040197389  SORCS1  sortilin related VPS10 domain containing receptor 1 Oryctolagus cuniculus

[Assa Yeroslaviz]

thanks, I was just now looking into efetch and esearch and tried to concatenate a pipeline for that. but you beat me to it. Thnaks again

[Assa Yeroslaviz]

Hi again, I'm not sure what elink should do, but with it in the command I don't get any results.

$ esearch -db nuccore -query 34809228 | elink -target gene | esummary | xtract -pattern DocumentSummary -element  Id,Caption,Organism

Here I get no results, but with this

$ esearch -db nuccore -query 34809228 | esummary | xtract -pattern DocumentSummary -element Id,Caption,Organism
34809228" term="34809228    AY386695    rabbit

[GenoMax]

You should have stayed away from GI numbers (if you had that option when you did your magicblast). gi numbers are deprecated for end-user use and this may be one of those examples where things don't work. We can get a result searching with that on NCBI site but the command line query does indeed not seem to be working reliably.

[Assa Yeroslaviz]

Yes, this is true, but we have to work with what we got. And I got stuck with the gi numbers :-( So I need to make the best out of it. I don't think magicblast can output something else. But thanks for the help.