Question: Annotating Trinity transcriptome assembly with BLAST
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gravatar for trish0401
2.3 years ago by
trish040110
trish040110 wrote:

I am working on my first sequencing project. I have used Trinity to make de novo assemblies of RNA-Seq libraries for ~ 8 primate species, including human. I am trying to figure out how to annotate the human transcriptome and want to use BLAST. I was hoping someone could help me out with how to generate a blast database in UNIX for my human sample, and then BLAST the Trinity.fa transcriptome against it.

Thanks in advance.

blast rna-seq • 1.1k views
ADD COMMENTlink modified 2.3 years ago by geek_y9.4k • written 2.3 years ago by trish040110
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gravatar for geek_y
2.3 years ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k wrote:

You could use Annocript or Trinotate

Annocript:

It executes several blast analysis steps and builds annotations using information taken from UniProt, NCBI Conserved Domain Database and Nucleotide divisions (CDD), Gene Ontology, and the Enzyme Commission.

Trinotate:

Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases).

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by geek_y9.4k
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