How to add blastx hit name to the related contigs of assembly?
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7.6 years ago
sohra ▴ 40

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 Assembly RNA-Seq blast • 1.9k views
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7.6 years ago
IsmailM ▴ 110

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...

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

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See edit...

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7.6 years ago

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

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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.

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