Annotating Proteins

Predicting function of proteins.

Finding homologs

For Protein to Protein searches BLASTP, phmmer (HMMER), FASTA

module load fasta
fasta36 query database > results.FASTA
fasta36 -m 8c -E 1e-3 query database > results.FASTA.tab

To Find Domains

See Overview lecture Domains lecture

Searching with HMMer against Pfam

See the HMMER tutorial

Searching with Interpro

Searching Interpro on HPCC

Note this can be slow.

#!/bin/bash -l
#SBATCH -p epyc -N 1 -n 1 -c 8 --mem 16G --time 24:00:00
#SBATCH -J iprscan
#SBATCH -o logs/%x.%j.log
module load iprscan

set -euo pipefail
CPU=${SLURM_CPUS_PER_TASK:-1}
interproscan.sh  --goterms --pathways -f tsv -i PROTEINFILE.fa --cpu $CPU > SEARCH.log

Run mkdir -p logs before submitting. See UNIX IV for how to choose -c, --mem and --time.

The results will contain information like

Gene Ontology http://geneontology.org/

Running Analyses on Biocluster 

# in a job script or an srun session with -c 4 (or more)
module load hmmer
module load db-pfam
CPU=${SLURM_CPUS_PER_TASK:-1}
hmmscan --cpu $CPU --domtblout domtbl_results.out $PFAM_DB/Pfam-A.hmm proteins.fa > proteins.hmmscan
hmmsearch --cpu $CPU --domtblout hmmsearch_domtbl_results.out $HMM protein-db.fa > protein.hmmsearch

Pfam2GO - http://current.geneontology.org/ontology/external2go/pfam2go

Workshop in class

Let’s compare the genomes of cyanobacteria and identify if there are differences in gene content based on Protein domains.

Many papers investigating the evolution and genomes of cyanobacteria.

  1. Searching for Pfam domains in a set of proteins from several species (start with 3)
    • Let’s download some genomes/proteomes from NCBI
  2. Parsing report files and count the number of domains per species (in python)
  3. Summarize the content comparing with a table sorted by counts