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All posts created by scaruso

| posted 15 Mar, 2024 18:18
Though it may no longer be relevant, SOSUI was down for a long time, but it seems to be working right now at this site:

Edited 15 Mar, 2024 18:18
Posted in: Functional AnnotationMembrane protein
| posted 30 Oct, 2023 01:27
Good evening all!

Does anyone have any news about Phage Enzyme Tools (PET2.0)? I have used it as part of my class for years and have noticed that it has been down for a few days.


Posted in: General Message BoardPhage Enzyme Tools - PET2.0 - Down?
| posted 01 Jul, 2023 22:33
Like in Cluster A and BD phages, the DNA primase of many cluster BF phages is split into two overlapping reading frames. The upstream portion of the gene may be missed by Glimmer and Genemark and may not be called in DNA Master.

As per the entries in Cluster A and BD: "We are not sure what happens within the cell during the infection to generate the correct full length primase, so for now, we add both parts to the annotations with a large overlap."
Posted in: Cluster BF Annotation TipsDNA Primase
| posted 11 Jun, 2023 14:06

I usually use DNAM for teaching and PECAAN for QC, but with the current DNAM connection issue, I may have to use PECAAN for teaching in a week or two in a class of 18. I can come up with something, but if I don't have to reinvent the wheel, I would rather not. So, does anyone have a way of teaching it/with it that they like and want to pass on?


Posted in: PECAANTeaching with PECAAN
| posted 03 Jun, 2023 15:13
Cluster BF phages have a terminase, small subunit on the right arm that has been recently identified, See RetrieverFever gp 78
Edited 03 Jun, 2023 15:14
Posted in: Cluster BF Annotation Tipsterminase, small subunit
| posted 11 May, 2023 19:12

OK. Thanks! I was worried about a summer isolated Bt phage and that I was getting a warning. I will keep on keeping on if we do anymore. Though we annotate Strep in the summer, too.


Posted in: DNA MasterGenBank Submissions
| posted 11 May, 2023 18:18

I am at one of the schools that not only sends phage genomes to PITT for submission, but occassionally submits to GenBank directly when we work on different species. We do so by emailing the submission file in right from DNAM with the appropriate information. Recently I received a note that there is a format change (see below) and I now wonder if requires a change I am unsure how to make.

If anyone can share any updates on this, I would be grateful.


You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn.
table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions.

We will process this tbl2asn submission. DO NOT resubmit it.
You will be contacted regarding its processing in a separate message, and you can complete any necessary changes to this submission as usual.

However, for future submissions, we encourage you to use the newer command line program table2asn to generate the appropriate .sqn file for submission.

Information about table2asn can be found at:

The values of a few arguments have changed compared to tbl2asn.
In particular:

Old New Purpose
- -help to get a summary of the command line arguments
-p -indir to use all the .fsa files in the specified directory as input
-r -outdir to deposit the output files in the specified directory
-Z <file> -Z to run the discrepancy report
-a r10k -gaps-min 10 to convert runs of 10 or more Ns to gaps of estimated size
Posted in: DNA MasterGenBank Submissions
| posted 25 Mar, 2022 03:17

There is certainly a history of that PHAM being called a holin:

TOPCONS shows it to have two TMDs and most of the internal tools agree, with the ones disagreeing showing one TMD.

HHPred doesn't show the TMDs, as you mention, but has a perfect PFAM hit to the holin: PFAM isn't the best, but it's a full length hit. And it's been called in lots and lots of places:

On one of ours, I would feel pretty comfortable with it.

I hope that's helpful,

Posted in: Cluster P Annotation TipsAssignment of gp28 as holin
| posted 22 Mar, 2022 15:01
Thank you!

Posted in: PECAANPECAAN not BLASTing?
| posted 21 Mar, 2022 14:14
Good morning all,

Has anyone noticed an issue with PECAAN running BLAST over the last week? I have checked the jobs table, and they haven't been changing. Is it down?

Posted in: PECAANPECAAN not BLASTing?