Acidovorax JS42 Parales Project: Difference between revisions

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== Objectives ==
Use whole genome sequencing to find mutations involve with the evolution of novel trains in Acidovorax JS42 (3- or 4-nitrotoluene metabolism)
== Genomes ==
== Genomes ==


454 400bp sequence unpaired
454 400bp sequence unpaired
Coverage ~8x


Genomes assembled with newbler and no-split option
Genomes assembled with newbler and no-split option
1. Assembled the contigs against the reference genome (aka syntenic path assembly)
# Assembled the contigs against the reference genome (aka syntenic path assembly)
a. Unordered: http://genomevolution.org/r/3ipl
## Unordered: http://genomevolution.org/r/3ipl
b. Ordered: http://genomevolution.org/r/3ipk
## Ordered: http://genomevolution.org/r/3ipk
c. Assembled: http://genomevolution.org/r/3ipn
## Assembled: http://genomevolution.org/r/3ipn
2. Annotated the genomes using
# Annotated the genomes using
a. Prodigal for protein coding genes
## Prodigal for protein coding genes
b. tRNAScan-SE for tRNAs
## tRNAScan-SE for tRNAs
c. Don't have a solution for rRNAs
## Don't have a solution for rRNAs
3. Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes
# Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes


You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link:
You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link:
http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42
http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42


== Objectives ==
==Polymorphisms==


*Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html
*Description of the table: http://genomevolution.org/wiki/index.php/PolyMFind


==Notes==
==Notes==
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US

Latest revision as of 19:37, 25 August 2011

Objectives

Use whole genome sequencing to find mutations involve with the evolution of novel trains in Acidovorax JS42 (3- or 4-nitrotoluene metabolism)

Genomes

454 400bp sequence unpaired Coverage ~8x

Genomes assembled with newbler and no-split option

  1. Assembled the contigs against the reference genome (aka syntenic path assembly)
    1. Unordered: http://genomevolution.org/r/3ipl
    2. Ordered: http://genomevolution.org/r/3ipk
    3. Assembled: http://genomevolution.org/r/3ipn
  2. Annotated the genomes using
    1. Prodigal for protein coding genes
    2. tRNAScan-SE for tRNAs
    3. Don't have a solution for rRNAs
  3. Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes

You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link: http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42

Polymorphisms

Notes

Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US

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