Acidovorax JS42 Parales Project: Difference between revisions
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== Genomes == | == Genomes == | ||
454 400bp sequence unpaired | |||
Genomes assembled with newbler and no-split option | |||
1. Assembled the contigs against the reference genome (aka syntenic path assembly) | |||
a. Unordered: http://genomevolution.org/r/3ipl | |||
b. Ordered: http://genomevolution.org/r/3ipk | |||
c. Assembled: http://genomevolution.org/r/3ipn | |||
2. Annotated the genomes using | |||
a. Prodigal for protein coding genes | |||
b. tRNAScan-SE for tRNAs | |||
c. 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 | |||
== Objectives == | == Objectives == | ||
Revision as of 19:32, 25 August 2011
Genomes
454 400bp sequence unpaired
Genomes assembled with newbler and no-split option 1. Assembled the contigs against the reference genome (aka syntenic path assembly) a. Unordered: http://genomevolution.org/r/3ipl b. Ordered: http://genomevolution.org/r/3ipk c. Assembled: http://genomevolution.org/r/3ipn 2. Annotated the genomes using a. Prodigal for protein coding genes b. tRNAScan-SE for tRNAs c. 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
Objectives
Notes
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US