SEA-PHAGES | PECAAN not showing Starterator and Pham info

Link to this post \| posted 19 Jul, 2021 10:38
MSMC	Is there a reason that PECAAN provides a link to the Starterator report and Pham page for some genomes, but not others? See screenshots below - Looper is a Gordonia phage, Eraser is an Arthro phage. Cheers, Evan 75Kb

Link to this post \| posted 21 Jul, 2021 17:28
cdshaffer	I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page. One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure.

Link to this post | posted 21 Jul, 2021 17:28

cdshaffer

I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page.

One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure.

Link to this post \| posted 21 Jul, 2021 18:16
MSMC	cdshaffer I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page. One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure. Thanks Chris! I've been going gene by gene in PhagesDB, which has wworked, but I'll try the admin page strategy as well.

Link to this post | posted 21 Jul, 2021 18:16

MSMC

cdshaffer
I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page.

One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure.

Thanks Chris! I've been going gene by gene in PhagesDB, which has wworked, but I'll try the admin page strategy as well.

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PECAAN not showing Starterator and Pham info