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.
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written
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trish0401 •
1 answer
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).
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