Question: Where can I find annotation of a wheat Unigene Build?
0
gravatar for anna.gordon
5.4 years ago by
anna.gordon0 wrote:

Hi there,

A bit of a basic question, i've used the latest Wheat (Triticum aestivum) Unigene build 63 as my "reference" genome to map Illumina single end sequences to so I can perform differential expression analyses. Each unique gene ID has this format eg: Ta_S61633485

 

I'm shocked that there seems to be no central repository for any accompanying GO annotation. There MUST be some somewhere surely? If you work on wheat and you know the answer, can you please please give me a pointer??

I've tried FAQs at plantdb, NCBI, cerealsdb, INRA, GrainGenes

 

Many thanks,

Anna

rna-seq • 1.9k views
ADD COMMENTlink modified 5.4 years ago by sbdk8260 • written 5.4 years ago by anna.gordon0
0
gravatar for komal.rathi
5.4 years ago by
komal.rathi3.5k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.5k wrote:

Have you looked at dbWFA (wheat functional annotation)? Check this link urgi.versailles.inra.fr/dbWFA/ and click on Transcript(s) annotation on the bottom left panel. You can paste your list of gene IDs and get the corresponding GO annotation. I just saw the latest annotations they have is for build #62. But I guess, it may not be very different between #62 & #63. 

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by komal.rathi3.5k
0
gravatar for anna.gordon
5.4 years ago by
anna.gordon0 wrote:

Hi there,

Many thanks for pointing that part of the page out to me - I hadn't spotted it. Unfortunately my gene IDs are returning "Transcript ID was not found" or "No hit" possibly because i've used a later Unigene build, but i'll email them directly to see if they've got some ideas..

Cheers,

 

Anna

 

Ta_S12857639
Ta_S12857704
Ta_S12858073
Ta_S12858139
Ta_S12858143
Ta_S12858227
Ta_S12858389
Ta_S12858483
Ta_S12858490
Ta_S12858540
ADD COMMENTlink written 5.4 years ago by anna.gordon0
0
gravatar for sbdk82
5.4 years ago by
sbdk8260
United States
sbdk8260 wrote:

I am not sure if this will help ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/

ADD COMMENTlink written 5.4 years ago by sbdk8260

I don't think it will. That's a fasta file, not an annotation file.

ADD REPLYlink written 5.4 years ago by komal.rathi3.5k
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