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Arthrobacter Annotations

| posted 22 Jan, 2016 20:17
Is there a consensus on how Arthrobacter annotations should be recorded? I am wondering about GeneMark and BLAST. Are we using GeneMArkS or A. aurescens? and NCBI BLAST or phagesdb BLAST? or both?
| posted 27 Jan, 2016 20:50
The best answer is all of the above!
I use GeneMarkS and GeneMark with Arthrobacter FB24. Whatever you use, record that in your cover sheet. The one directed at self is the same info as what comes in through the auto-annotation, just in picture form. So it is not additional info. Both GeneMark against self and against a host are helpful and informative. Blasting against phagesDB (and Phamerator - which is the same data) is just identifying what we already know. Now that we have >45 Arthrobacter phage genomes finalized and in GenBank, you should find more helpful info there. However, I will always say you should run an NCBI BLast because there is always new data being posted there. Likewise, HHPred should be run with the 3 databases pbd70_, pfamA_, and tigrfam_. Again new data is showing up there regularly and we are able to identify more functions to our genes than ever before.
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