GEN220_2023

2023 Class

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Annotating Proteins

Predicting function of proteins.

• Pfam site docs
• Pfam manual

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

Searchin Interpro on HPCC

Note this can be slow.

#SBATCH -p batch -N 1 -n 8
module load iprscan
CPU=4
interproscan.sh  --goterms --pathways -f tsv -i PROTEINFILE.fa --cpu $CPU > SEARCH.log

The results will contain information like

Gene Ontology http://geneontology.org/

Running Analyses on Biocluster

module load hmmer
module load db-pfam
hmmscan --domtbl domtbl_results.out $PFAM_DB/Pfam-A.hmm proteins.fa > proteins.hmmscan
hmmsearch --domtbl domtbl_results.out $HMM protein-db.fa > protein.hmmsearch

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

Workshop

1. Searching for Pfam domains in sets of proteins - Bioinformatics_4 See search_SOD1.sh
2. Parsing report files