Team I Functional Annotation Group: Difference between revisions

From Compgenomics 2018
Jump to navigation Jump to search
Wenyi Qiu (talk | contribs)
Wenyi Qiu (talk | contribs)
Line 20: Line 20:


'''LipoP'''
'''LipoP'''
Command:  
Command:  
<pre>LipoP -<output_format> -<input_file> <output_file></pre>
<pre>LipoP -<output_format> -<input_file> <output_file></pre>
Line 25: Line 26:


'''TMHMM'''
'''TMHMM'''
Command:
Command:
<pre>tmhmm -<output_format> -<input_file> <output_file></pre>
<pre>tmhmm -<output_format> -<input_file> <output_file></pre>
Line 30: Line 32:


'''SignalP'''
'''SignalP'''
Command:  
Command:  
<pre>signalp -t <organism_type> -f <output_format> <input_file></pre>
<pre>signalp -t <organism_type> -f <output_format> <input_file></pre>
Runtime: ~ 4mins /genome
Runtime: ~ 4mins /genome
'''DeepARG'''
Command:
<pre>
'''Interproscan'''


=='''Result'''==
=='''Result'''==


=='''Reference'''==
=='''Reference'''==

Revision as of 14:54, 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

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