Siphoviridae was not detected in metagenomic analysis

apcamargo / genomad

geNomad: Identification of mobile genetic elements

https://portal.nersc.gov/genomad/

Other

169 stars 17 forks source link

Siphoviridae was not detected in metagenomic analysis #5

Closed mijiandui closed 1 year ago

mijiandui commented 1 year ago

DearJamie Morton，

  Thanks a lot for your excellent software. However, we found  Siphoviridae was the majority one in the gut of previous studies. But we did not find it in our result with the software analysis. And we check the list ICTV VMR_19 and also did not found any more. Siphoviridae was removed? Could you please help me. Siphoviridae was combined to which order or family?
   Thanks a lot.
   Warm Regards
   Jiandui Mi

apcamargo commented 1 year ago

Hey @mijiandui,

Yeah, Siphoviridae are not recognized anymore. This family was originally defined using morphological data, but this classification doesn't mirror viral evolution (see here: https://www.mdpi.com/1999-4915/13/3/506/htm).

Most tailed phages in metagenomes actually belong to non-described families, so it is pretty common to have sequences assigned to the class level (Caudoviricetes).