Name: hmm_proteome_annotation
Owner: The Marcotte Lab
Description: null
Created: 2016-04-15 00:45:35.0
Updated: 2016-04-20 04:21:20.0
Pushed: 2017-01-12 18:48:05.0
Homepage: null
Size: 108798
Language: Shell
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This is a process for sorting a whole proteome into Hmm profiles using hmmscan. outputs:
Instructions 1.Place the annotation and hmm files for a phylogenetic level in hmms/
ex. euNOG_hmm.tar.gz euNOG.annotations.tsv.gz
HMM profiles come from http://eggnogdb.embl.de/#/app/downloads
2.From the main directory run: bash masterscripts/startPress.sh [level]
ex. bash masterscripts/startPress.sh euNOG
This step takes about 10 TACC minutes
Make a directory for the species that you want to run in proteomes/ ex. mkdir proteomes/arath
Place the species' fasta in its folder in proteomes/ ex. proteomes/arath/uniprot-proteome%3AUP000006548.fasta
After the hmms are pressed, from the main directory run: bash masterscripts/startHmmscan.sh [species] [proteome] [level]
ex. bash master_scripts/startHmmscan.sh arath proteomes/arath/uniprot-proteome%3AUP000006548.fasta euNOG
This step takes up to 20 TACC hours depending on proteome/hmm profile count
tophit + nonhits are combined to create look ups for the othology mass spec analysis