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All posts created by welkin

| posted 13 Apr, 2018 22:19
Cluster DF phages contain a recombinase in the right arm that is related to the integrase genes of temperate phages. However, these phages do not appear to contain any of the rest of the necessary machinery for lysogeny (attP, immunity repressor, etc); and so we believe these are not integrases, but rather recombinases, and should be labeled as such.
Posted in: Cluster DF Annotation Tipsnot an integrase
| posted 13 Apr, 2018 22:17
Lysin A, which is a single multi-domain protein in many Actinobacteriophages, is split at the domain boundaries encoded by two adjacent genes in members of cluster DF. The functions should be reported as "lysin A, whatever the domain is" to indicate that each gene does not encode the full lysin A.
Posted in: Cluster DF Annotation Tipslysin A in two parts
| posted 13 Apr, 2018 22:15
Cluster DF contains some phages that were not isolated and sequenced by the SEA-PHAGES program. Their finders chose a different bp1 than we did, and annotated their genomes differently. We do not curate, update, or QC these genomes.

These phages are:
Gmala1, GordDuk1, GordTnk2, and GMA3
Posted in: Cluster DF Annotation Tipsnon SEA-PHAGES genomes
| posted 13 Apr, 2018 22:11
Cluster DE contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders annotated their genomes differently. We do not curate, update, or QC this genome.

This phage is:
GTE6
Edited 13 Apr, 2018 22:11
Posted in: Cluster DE Annotation Tipsnon SEA-PHAGES genomes
| posted 13 Apr, 2018 22:08
Some Cluster DC phages, like Twister6, contain two integrase genes in the central portion of the genome.
Posted in: Cluster DC Annotation Tipstwo integrases
| posted 13 Apr, 2018 22:02
Cluster DB phages are very plastic in the middle of the genome, near the integration cassette. Some, like Bowser, contain two integrase genes in this region.
Posted in: Cluster DB Annotation Tipstwo integrases
| posted 13 Apr, 2018 21:58
Lysin A, which is a single multi-domain protein in many Actinobacteriophages, is split at the domain boundaries encoded by two adjacent genes in SOME members of cluster CZ. The functions should be reported as "lysin A, whatever the domain is" to indicate that each gene does not encode the full lysin A.
Posted in: Cluster CZ Annotation Tipslysin A in two parts SOMETIMES
| posted 13 Apr, 2018 21:55
There is a final HNH endonuclease gene at the end of CY genomes that is not predicted by the gene prediction programs.
Posted in: Cluster CY Annotation TipsFinal HNH
| posted 13 Apr, 2018 21:52
Cluster CZ phages are very plastic in the middle of the genome, near the integration cassette. Some, like Howe, contain two integrase genes in this region.
Posted in: Cluster CZ Annotation Tipstwo integrases
| posted 13 Apr, 2018 21:51
Cluster CY phages are very plastic in the middle of the genome, near the integration cassette. Some contain two integrase genes in this region.
Edited 13 Apr, 2018 21:51
Posted in: Cluster CY Annotation Tipstwo integrases