Gene prediction

de novo gene prediction Augustus

Functional annotation

1. genome
2. organellar genome
3. transcriptome

blast

hmmer

1. Basic usage (???)

2. Searching proteins.fasta with hmm profiles

There is a pair of scripts in /home/halakuc/scripts:

• hmmer_them_all.sh Usage: hmmer_them_all.sh -p proteins.fasta –profiles profile1.hmm [profile#.hmm] -o outdir
• hmmer_parser.py Helper script for the first one.

They produce following output (in outdir):

• proteins_profile#.out - text output of hmmer
• proteins_profile#.tblout - table output of hmmer
• proteins_interesting.fasta - fasta containing all significant hits, header contains protein name and hmmer profile name

kegg

pfam