Team I Functional Annotation Group: Difference between revisions
Jump to navigation
Jump to search
| Line 18: | Line 18: | ||
'''Eggnog''' | '''Eggnog''' | ||
'''PilerCR''' | |||
Command: | |||
<pre>pilercr -in <input_file> -out <output_file></pre> | |||
Runtime: <5 sec/genome | |||
'''Phobius''' | |||
Command: | |||
<pre>phobius.pl -<output_format> <input_file> > <output_file></pre> | |||
'''LipoP''' | '''LipoP''' | ||
Revision as of 14:59, 9 April 2018
Introduction
Background
Functional annotation is the process of locating genes and identifying their functions (biochemical functions, regulatory functions, etc.) in the genome.
Objective
- Fully annotate 258 genomes from Gene Prediction group, focusing on antibiotic resistance
- Provide Comparative Genomics group with data required to perform Genome Wide Association Study(GWAS)
Pipeline
Tools
Prokka
Command:
prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> --rfam --rnammer <input_file>
Runtime: ~ 16mins /genome
Eggnog
PilerCR
Command:
pilercr -in <input_file> -out <output_file>
Runtime: <5 sec/genome
Phobius
Command:
phobius.pl -<output_format> <input_file> > <output_file>
LipoP
Command:
LipoP -<output_format> -<input_file> <output_file>
Runtime: ~2mins /genome
TMHMM
Command:
tmhmm -<output_format> -<input_file> <output_file>
Runtime: ~6mins /genome
SignalP
Command:
signalp -t <organism_type> -f <output_format> <input_file>
Runtime: ~ 4mins /genome
DeepARG
Command:
Interproscan