Team I Functional Annotation Group: Difference between revisions

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'''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

Result

Reference