Team II Functional Annotation Group

Introduction

Data

We are given 258 assembled genomes and predicted genes of Klebsiella spp.

Approach

Functional Annotation utilizes computational methods to functionally annotate 258 Klebsiella genomes. The approach should be scalable, reduce query size and reduce database size. Two classes of methods are generally adopted: ab-initio and homology-based.

Non-coding RNA

rRNA, tRNA, and sRNA

Please refer to "Team II Gene Prediction Group - RNA Prediction" [1]

CRISPR

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) are found in approximately 40% of sequenced bacterial genomes. They are reported to be related to Bacterial immunity regulation, cell defense mechanism, DNA rearrangement, replication, and regulation. And Klebsiella has an unusually high proportion of self-targeting spacers

Tool

Version: Piler-CR 1.06
PILER-CR is a program which specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly and has both high sensitivity and high specificity.

Input: FASTA

Output: Piler-CR specific report format

Performance by using reference genome:

Run-time: ~5 seconds for a 5Mb genome
CRISPR found:2

Others

Prophage Genes

Prophage genes are a bacteriophage genetic materials integrated into bacterial DNA genome or existing plasmid. This requires phages in latent phase that the viral genes are present in the bacterium without causing disruption of the bacterial cell. In fact, prophage genes are one of the major source of new genes and functions in bacterial genomes[2], such as antibiotic resistance[3], virulence factor[4], and biofilm formation[5].

PHASTER

PHASTER (PHAge Search Tool Enhanced Release)[6] is a server for the rapid identification and annotation of prophage sequences in bacterial genomes and plasmids. It takes both assembled genome (with or without contigs) or GenBank file and compares to their viral and bacterial databases[7]

Input: FASTA or GenBank

Output: PHASTER specific report format

Performance by using reference genome:

Run-time: ~5min for a 5Mb assembled genome
Phage Region Found: 8 using NC_016845.1 Klebsiella pneumoniae reference genome