LOMETS Overview

Given a FASTA-format protein sequence, LOMETS finds homologous protein structures that could be used for threading.

LOMETS output files (or equivalent) are required as input for findsitemetal.

Quick Reference

Helper scripts at: /n/groups/drad/julian/LOMETS_helpers/.

Basically, just run /n/groups/drad/julian/LOMETS_helpers/make_lomets_scripts_full.sh in the directory you want your LOMETS jobs to live in and give a list of uniprot IDs as input.

For example: bash make_lomets_scripts.sh protein_ids "1500M" "00-06:00" "short".

That script will download all uniprot IDs from UniProt directly. If you suspect that some of your IDs can't be downloaded from uniprot, then:

• Use the /n/groups/drad/julian/LOMETS_helpers/get_ups_from_uniprot.sh to download all IDs that can be found on uniprot
• Write a custom script to make job folders for the other sequences
• Make a list of all IDs that you want to make scripts for
• Run /n/groups/drad/julian/LOMETS_helpers/make_lomets_scripts.sh in the same manner.