Team I Functional Annotation Group: Difference between revisions

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Command:  
Command:  
<pre>prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> <input_file> </pre>
<pre>prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> --rfam --rnammer <input_file> </pre>
Runtime: ~ 16mins /genome


'''Eggnog'''
'''Eggnog'''


'''LipoP'''
'''LipoP'''
Command:
<pre>LipoP -<output_format> -<input_file> <output_file></pre>
Runtime: ~2mins /genome
'''TMHMM'''
Command:
<pre>tmhmm -<output_format> -<input_file> <output_file></pre>
Runtime: ~6mins /genome


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


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


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

Revision as of 14:51, 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

Result

Reference