Team II Functional Annotation Group: Difference between revisions
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===Virulence Factors=== | ===Virulence Factors=== | ||
===Prophage Genes=== | ===Prophage Genes=== | ||
===PHASTER=== | 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[https://www.sciencedirect.com/science/article/pii/B9780123944382000049] | ||
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<br> | 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<br> | ||
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Revision as of 22:58, 6 April 2018
Introduction
Functional Annotation
Data
We are given 258 assembled genomes and predicted genes of Klebsiella spp.
Approach
Protein-Coding Regions
Signaling Peptides
Transmembrane Regions
Lipoproteins
Operons
Pathways
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
Performance by using reference genome:
Run-time: ~5 seconds for a 5Mb genome
CRISPR found:2
Others
Antibiotic Resistance
Virulence Factors
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
Performance by using reference genome:
Run-time: ~5 seconds for a 5Mb genome
CRISPR found:2