SEA-PHAGES | Data on tRNAs for many phages?

Link to this post \| posted 28 Oct, 2022 21:15
afreise	Hello, My students are interested in evaluating the presence and number of tRNAs in entire clusters of phages. However, the phagesDB data on tRNAs is often not up to date - it seems like this must be entered manually in a phage's page even after a phage has been finished in Genbank. For example, in Rhodococcus phages, Phamerator suggested that over 40 of the phages had tRNAs, but phagesDB lists almost no phages with tRNAs for that host. Is this something that could be updated automatically after final annotation is complete? And in the meantime, is there an easy way to pull accurate tRNA numbers/prsence for phages across a cluster and/or host? Thanks, Amanda

Link to this post | posted 28 Oct, 2022 21:15

Hello,

My students are interested in evaluating the presence and number of tRNAs in entire clusters of phages. However, the phagesDB data on tRNAs is often not up to date - it seems like this must be entered manually in a phage's page even after a phage has been finished in Genbank. For example, in Rhodococcus phages, Phamerator suggested that over 40 of the phages had tRNAs, but phagesDB lists almost no phages with tRNAs for that host.

Is this something that could be updated automatically after final annotation is complete? And in the meantime, is there an easy way to pull accurate tRNA numbers/prsence for phages across a cluster and/or host?

Thanks,
Amanda

Link to this post \| posted 30 Oct, 2022 13:16
chg60	Hi Amanda, This is another good use case for a quick MySQL export command. This one may be a bit more complicated than the one I gave you for exporting phams, but will allow you to count the annotated tRNAs. mysql -u root -p Actino_Draft -e "SELECT PhageID, Start, Stop, Orientation, AminoAcid, Anticodon FROM trna WHERE PhageID IN (SELECT PhageID FROM phage WHERE HostGenus = 'Rhodococcus' ) ORDER BY PhageID, Start ASC;" -B -N > ~/Rhodo_trnas.tsv If you want to filter on a different host, you can change from 'Rhodococcus' to 'Othergenus'. If you want to filter on one or more clusters, substitute WHERE HostGenus = 'Rhodococcus' for WHERE Cluster in ('Choose', 'your', 'clusters' ) Note that the fact that one or more tRNAs have not been annotated in a particular phage does not mean that they aren't there, only that the most recent annotation did not include them. More comprehensive studies of tRNAs should always begin by re-annotating tRNAs in the strains of interest. Best, Christian Edited 30 Oct, 2022 13:18 6Kb

Link to this post | posted 30 Oct, 2022 13:16

chg60

Hi Amanda,

This is another good use case for a quick MySQL export command. This one may be a bit more complicated than the one I gave you for exporting phams, but will allow you to count the annotated tRNAs.

mysql -u root -p Actino_Draft -e "SELECT PhageID, Start, Stop, Orientation, AminoAcid, Anticodon FROM trna WHERE PhageID IN (SELECT PhageID FROM phage WHERE HostGenus = 'Rhodococcus' ) ORDER BY PhageID, Start ASC;" -B -N > ~/Rhodo_trnas.tsv

If you want to filter on a different host, you can change from 'Rhodococcus' to 'Othergenus'.

If you want to filter on one or more clusters, substitute

WHERE HostGenus = 'Rhodococcus'

for

WHERE Cluster in ('Choose', 'your', 'clusters' )

Note that the fact that one or more tRNAs have not been annotated in a particular phage does not mean that they aren't there, only that the most recent annotation did not include them. More comprehensive studies of tRNAs should always begin by re-annotating tRNAs in the strains of interest.

Best,

Christian

Edited 30 Oct, 2022 13:18

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Data on tRNAs for many phages?