Team II Functional Annotation Group

Introduction

Data

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

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]

Inserted prophage genes have lots of features, including antibiotic resistance

PHASTER

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

Input: FASTA

Output: Piler-CR specific report format

Performance by using reference genome:

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