SEA-PHAGES | Pham not found in Starterator

Link to this post \| posted 11 Nov, 2021 22:55
cdshaffer	OK follow up on the issue with pham 56633. As I said before I had already found that the issue was with phage ISF9 gene 29. It turns out that phage is one of the "Added phage" which don't come from any of the Pittsburg programs but was a phage isolated from Microbacterium oxydans in Iran and published in genbank. It turns out this sequence has two N bases in the version of the sequence in Actino_Draft and these N bases confused Starterator and caused it to crash when it was counting bases to find the start and stop codons. So this bug should not be a problem for phage that we publish since Dan is always careful to check the sequences for N's but it could be an ongoing issue for these phage that get added. Not sure exactly how to deal with these phage in the long run but for now please continue to post if you find a missing pham report.

Link to this post | posted 11 Nov, 2021 22:55

OK follow up on the issue with pham 56633. As I said before I had already found that the issue was with phage ISF9 gene 29. It turns out that phage is one of the "Added phage" which don't come from any of the Pittsburg programs but was a phage isolated from Microbacterium oxydans in Iran and published in genbank. It turns out this sequence has two N bases in the version of the sequence in Actino_Draft and these N bases confused Starterator and caused it to crash when it was counting bases to find the start and stop codons. So this bug should not be a problem for phage that we publish since Dan is always careful to check the sequences for N's but it could be an ongoing issue for these phage that get added. Not sure exactly how to deal with these phage in the long run but for now please continue to post if you find a missing pham report.

Link to this post \| posted 11 Apr, 2022 14:19
andrea	Good morning, We are not able to access Pham 103037 on phagesdb.org or PECAAN. We've been trying since Wednesday, 4/6. Thank you! Andrea

Link to this post \| posted 11 Apr, 2022 15:39
debbie	There is a human element in the processing of Starterator reports. It should appear soon. Thank you for your patience. debbie

Link to this post \| posted 11 Apr, 2022 16:15
andrea	Thanks for letting us know Debbie! We appreciate it.

Link to this post \| posted 11 Apr, 2022 19:38
cdshaffer	I am looking into this. Starterator is currently at the most recent database release which means this pham must have failed analysis. This has been happening more and more as the database gets more entries that are not analyzed using the SEA-PHAGES protocol. These other sources of annotation often create gene models that have some kind of weird property (like a start codon other than ATG, GTG or TTG). While I look into why the failure and try to correct for it, if you tell me which gene/phage you are looking for, I can probably find it in one of the older versions of the database for you.

Link to this post | posted 11 Apr, 2022 19:38

cdshaffer

I am looking into this. Starterator is currently at the most recent database release which means this pham must have failed analysis. This has been happening more and more as the database gets more entries that are not analyzed using the SEA-PHAGES protocol. These other sources of annotation often create gene models that have some kind of weird property (like a start codon other than ATG, GTG or TTG).

While I look into why the failure and try to correct for it, if you tell me which gene/phage you are looking for, I can probably find it in one of the older versions of the database for you.

Link to this post \| posted 11 Apr, 2022 20:39
cdshaffer	Ok, I just reran pham 103037 and it ran without a hitch, so I have no idea why it failed in the automatted pipeline. Could be a weird one-off quirk or something more serious. Please let me know if you have any more trouble. Here is the link for your convenience; http://phages.wustl.edu/starterator/Pham103037Report.pdf

Link to this post \| posted 11 Apr, 2022 20:58
andrea	Got it! Thanks so much. It's for GoldenAsh_3.

Link to this post \| posted 02 Mar, 2023 21:22
atenea	Hello, We are working on Milani and Genes 6 and 7 do not have a starterator report. The information says they are Orphams. How should we proceed with this information? Are these genes unique to Milani?

Link to this post \| posted 02 Mar, 2023 21:22
atenea	Hello, We are working on Milani and Genes 6 and 7 do not have a starterator report. The information says they are Orphams. How should we proceed with this information? Are these genes unique to Milani?

Link to this post \| posted 03 Mar, 2023 16:45
cdshaffer	Unfortunately, being an "Orpham" means that the protein has not other similar proteins and is thus placed in its own pham group. Starterator is about using evidence from evolution to help gather evidence for start codons based on conservation and evolution of the genes by comparing how they have evolved over time. However for orphams, with only one member in the pham, there is nothing to "compare", so there is nothing to report. Start codon choice will just have to proceed without evidence from comparative evolution and rely on what evidence is available.

Link to this post | posted 03 Mar, 2023 16:45

cdshaffer

Unfortunately, being an "Orpham" means that the protein has not other similar proteins and is thus placed in its own pham group. Starterator is about using evidence from evolution to help gather evidence for start codons based on conservation and evolution of the genes by comparing how they have evolved over time. However for orphams, with only one member in the pham, there is nothing to "compare", so there is nothing to report. Start codon choice will just have to proceed without evidence from comparative evolution and rely on what evidence is available.

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Pham not found in Starterator