Team II Functional Annotation Group: Difference between revisions
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===Virulence Factors=== | ===Virulence Factors=== | ||
===Prophage Genes=== | ===Prophage Genes=== | ||
===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> | |||
====Tool==== | |||
Version: Piler-CR 1.06 <br> | |||
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. | |||
<div style="border: 1pt dashed black; background : grey; padding: 1em 1em;"> | |||
Input: FASTA<br> | |||
Output: Piler-CR specific report format </div> | |||
Performance by using reference genome:<br> | |||
<div style="border: 1pt dashed black; background : grey; padding: 1em 1em;"> | |||
Run-time: ~5 seconds for a 5Mb genome<br> | |||
CRISPR found:2 | |||
</div> | |||
==Final Pipeline== | ==Final Pipeline== | ||
Revision as of 22:38, 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
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
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