Phrann_Cover_Letter.txt
SCSU

One gene (formerly known as Phrann_gp13) was deleted that had no coding potential, and was a lone reverse strand gene. It's pham had only one other member which is also a draft sequence N cluster phage (Panchino).

Phrann_gp30 has strong hits to M.tuberculosis genes of NKF, but there is a better glob of coding potential on the -1 reading frame. This ORF would significantly overlap with the 3'end of the Phrann_gp29 gene.

Deleted Phrann_gp34 (as labelled in Draft Phamerator) since it overlaps with a gene on the opposite strand which does resemble another protein family with conserved domain DUF2335/COG5346/Pfam 10097 Domain of unknown function. This gp34 had only 1 other pham member which is a draft annotation (Purky- P cluster)

Upstream of Phrann_gp35 (between gp35 & gp36) is a fairly large gap of 190bp. There doesn't seem to be any good-looking ORF's there.

Phrann_gp58: The start site was chosen that did not agree with Genemark or Glimmer, but aligned 1:1 with another phage, and was a compromise between ORF length and a good SD score. 

Deleted Phrann_gp68 (on Phamerator draft seq), since it had a large overlap with gene on the opposite strand, NKF, NO CODING POTENTIAL, and only called as a pham based on 3 other draft sequences.

In the +2 frame at 43538, there is a good looking little ORF that overlaps the penultimate gene. It is not called, but the SD=-3.796, Zvalue=2.935. Almost looks like two overlapping ORFs, or a programmed translational frameshift, or some left over concatenation of two genes. 

Other than that we are confident with the annotation.