Acidovorax JS42 Parales Project

Objectives

Sept. 2nd 2011

Overall goals:

1. ID functional polymorphisms with low false negative rate and low false positive rate
2. Support upcoming KJS metabolism paper using strains 2 and 4

Becky:

1. Budget for more sequencing
2. Number of new strains to sequence
3. Gene list organized by operon/pathway section for upcoming paper

From Becky

Ajs 204: a GntR-type regulator; snp changing R to W in KSJ4 
Ajs 205: a sigma 54; snp changing A to T in KSJ2
Ajs 205: a sigma 54; deletion frameshift in KSJ4

And I assume the deletion in the string of Gs in Ajs 205 in KSJ4 may be a sequencing error. 
Am I missing anything? If that's it, I guess that would be a pretty easy line in the paper...

1. Validated polymorphisms from (3) in KSJ2 and KSJ4 (unless those are in a previous email)

Eric:

1. Fold-coverage of prior strain sequencing

##Is more coverage/different technology going to help reduce false positive rate?

1. 1. single strain unique polymorphism tables

## Focus on gene list provided in Becky(3) ## Check polymorphisms provided in Becky(4)

1. New sequencing:

## Which technology will be appropriate for upping coverage ## Which technology will be most cost-effective for sequencing new strains ## For different sequencing center tech: ### Cost (consider that prior KJS strain libraries are prepped for 454) ### Amount of data ### Lengh of reads ### wait-time for sequences