Question: How to add blastx hit name to the related contigs of assembly?
0
gravatar for sohra
4.8 years ago by
sohra40
Switzerland
sohra40 wrote:

Hello experts,

I'm quite new here, I did de novo transcriptome assembly and blastx against nr and uniprot databases. Could you please let me know how I should map the blastx results with de novo assembled contigs, my mean is adding annotation to this assembly?

thanks

sequencing blast rna-seq assembly • 1.5k views
ADD COMMENTlink modified 4.7 years ago • written 4.8 years ago by sohra40
1
gravatar for IsmailM
4.8 years ago by
IsmailM110
UK/London/University College London
IsmailM110 wrote:

Take a detailed look at http://www.marcottelab.org/users/BIO337_2014/EukGeneAnnotation.pdf

Personally I wouldn’t use blast for annotating an assembly - Have you had a look at Augustus?

EDIT

Transcriptome Annotation 

Have you seen https://trinotate.github.io/

You can input your blast results (and HMMER etc.) to get your annotated output...

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by IsmailM110

Thanks, but my mean is transcriptome assembly not genome assembly.

ADD REPLYlink written 4.8 years ago by sohra40

See edit...

ADD REPLYlink written 4.8 years ago by IsmailM110
1
gravatar for geek_y
4.8 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

Annocript is also a good tool for annotating transcripts.  See the Methods section of more details.

ADD COMMENTlink written 4.8 years ago by geek_y11k

Thanks for comments. I have already made blastx of contig against some databases. Now, my question is: is there any way to add the blast hit name to the header name of corresponding contig? actually, I would like to have contig_1 protein A, contig_2 protein 3, etc.

ADD REPLYlink written 4.7 years ago by sohra40
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