Acidovorax JS42 Parales Project: Difference between revisions
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Genomes assembled with newbler and no-split option | Genomes assembled with newbler and no-split option | ||
# Assembled the contigs against the reference genome (aka syntenic path assembly) | # Assembled the contigs against the reference genome (aka syntenic path assembly) | ||
## Unordered: http://genomevolution.org/r/3ipl | |||
## Ordered: http://genomevolution.org/r/3ipk | |||
## Assembled: http://genomevolution.org/r/3ipn | |||
# Annotated the genomes using | # Annotated the genomes using | ||
## Prodigal for protein coding genes | |||
## tRNAScan-SE for tRNAs | |||
## Don't have a solution for rRNAs | |||
# 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 | ||
| Line 23: | Line 23: | ||
==Polymorphisms== | ==Polymorphisms== | ||
Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html | *Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html | ||
Description of the table: http://genomevolution.org/wiki/index.php/PolyMFind | *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
- Assembled the contigs against the reference genome (aka syntenic path assembly)
- Unordered: http://genomevolution.org/r/3ipl
- Ordered: http://genomevolution.org/r/3ipk
- Assembled: http://genomevolution.org/r/3ipn
- Annotated the genomes using
- Prodigal for protein coding genes
- tRNAScan-SE for tRNAs
- Don't have a solution for rRNAs
- 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
- Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html
- Description of the table: http://genomevolution.org/wiki/index.php/PolyMFind
Notes
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US