Question: Annotating Trinity transcriptome assembly with BLAST
gravatar for trish0401
3.7 years ago by
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 • 1.7k views
ADD COMMENTlink modified 3.7 years ago by geek_y11k • written 3.7 years ago by trish040110
gravatar for geek_y
3.7 years ago by
geek_y11k wrote:

You could use Annocript or Trinotate


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 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 3.7 years ago • written 3.7 years ago by geek_y11k
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