SEA-PHAGES | Phage Clustering

Phage Clustering

Link to this post \| posted 07 Mar, 2024 20:43
bthomas7	Does anyone have any experience in defining how Phage are clustered? Also, is it possible that there is a link between geographic location and phage clustering? Any information or resources on these subjects would be greatly appreciated.

Link to this post \| posted 08 Mar, 2024 00:32
DanRussell	Way back in our "60 phage paper", we grouped phages into clusters based on > 50% nucleotide similarity. Of course, exactly what "50% nucleotide similarity" meant depended on which metrics in particular you looked at, so we used several different ones. You can read about them in the paper. More recently, we've moved to comparing genes rather than nucleotides, and have used ~35% Gene Content Similarity to put phages into clusters. Now, we're probably moving towards using a metric called Protein Equivalence Quotient to cluster phages. It's an ongoing process, and there is no "right" answer and phages will always challenge us by not neatly fitting into bins. PhamClust paper There have been a few groups who have looked at geography, and though there doesn't seem to be any high-level correlation between geography and type of phages found, some subclusters or even genes have only been found in certain geographical areas. –Dan

Link to this post | posted 08 Mar, 2024 00:32

DanRussell

Way back in our "60 phage paper", we grouped phages into clusters based on > 50% nucleotide similarity. Of course, exactly what "50% nucleotide similarity" meant depended on which metrics in particular you looked at, so we used several different ones. You can read about them in the paper.

More recently, we've moved to comparing genes rather than nucleotides, and have used ~35% Gene Content Similarity to put phages into clusters.

Now, we're probably moving towards using a metric called Protein Equivalence Quotient to cluster phages. It's an ongoing process, and there is no "right" answer and phages will always challenge us by not neatly fitting into bins.
PhamClust paper

There have been a few groups who have looked at geography, and though there doesn't seem to be any high-level correlation between geography and type of phages found, some subclusters or even genes have only been found in certain geographical areas.

–Dan

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Phage Clustering