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All posts created by ptsourkas

| posted 12 Jan, 2022 22:10
Glad you found it useful. Thanks for sharing!
Posted in: General Message BoardNew annotation software
| posted 10 Jan, 2022 23:24
Hello everyone, I would like to introduce Phage Commander, a new genome annotation tool developed in our lab. Phage Commander is designed to make genome annotation with multiple gene calling programs easier, faster, and less error prone. While DNA Master includes Glimmer and GeneMark for gene calling, we all know how tedious it is to use additional gene calling programs other than those two. To this end, we created Phage Commander, a program that runs a genome through multiple gene calling programs simultaneously. Phage Commander bundles the following programs: Glimmer, GeneMark, host-trained GeneMark.hmm, GeneMark S, GeneMark with Heuristics, GeneMark S2, Prodigal, RAST, MetaGene, and Aragorn. Genes and their coordinates are output to a single spreadsheet for easy visualization; genes are color coded based on how many programs call them. The results can be exported in GenBank formatted files (.gb), for import and further processing in DNA Master. Once in DNA Master, it's as if DNA Master included more gene calling programs than just Glimmer and GeneMark. Phage Commander is super easy to install and use, and runs on Mac, Windows and Linux. It can be downloaded here:
A publication describing Phage Commander has been published in Phage: Therapy, Applications and Research:

Phage Commander has been used by the SEA-PHAGES class at UNLV and the students and instructors love it. It is very easy to use, but feel free to shoot me an email anyimte if you have any questions or issues.

Edited 10 Jan, 2022 23:37
Posted in: General Message BoardNew annotation software
| posted 16 Jan, 2020 01:19
Hello everyone,

I'd like to present my new paper on annotation of phage genomes, entitled "A Method for Improving the Accuracy and Eciency of Bacteriophage Genome Annotation". In this paper, I present the method we use in my lab to annotate phage genome. It is based on the method we all use in SEA-PHAGES, but is a little more formal and detailed. I estimate the accuracy of the method and compare it to programs such as Glimmer and GeneMark, using the genomes of phages Lambda and Patience as test sets. It does seem that manual annotation method produces more accurate annotations, both in terms of gene calling and start codon calling, at least as far as Lambda and Patience are concerned. I think those of you interested in genome annotation will find this paper very interesting, and may find many useful things to incorporate into your annotation protocols.

Edited 16 Jan, 2020 01:24
Posted in: General Message BoardNew annotation method paper
| posted 26 Mar, 2019 15:34
Hi Debbie, and thanks for looking into this. I looked into the small forward ORF you mentioned but I feel the coding potential for that one is very weak, and it is more likely that gene 105 should be called long instead (which would fill the gap somewhat).
Posted in: Gene or not a GeneForward or reverse gene?
| posted 26 Mar, 2019 14:59
Yes, I got the next forward gene and deleted those short reverse genes (121-125). Thanks for looking into this.
Posted in: Frameshifts and IntronsPossible translational frameshift in Cluster J
| posted 25 Mar, 2019 23:19
Gene 103 (forward frame 3, 61983-62291) in cluster J phage NihilNomen is called by Glimmer and GeneMark (the GeneMark in DNA Master) and has strong coding potential for part of its length. While ordinarily this would be a no brainer, there is an ORF in reverse frame 1 (62040-62480) with equally strong coding potential and called by host-trained GeneMark.hmm and GeneMark S. The two genes overlap, but not completely (see attached figure).

In terms of homology matches, gene 103 has 6 matches to cluster J phages, while the reverse ORF has none.

Call both genes? Or just gene 103?
Posted in: Gene or not a GeneForward or reverse gene?
| posted 25 Mar, 2019 22:56
I have a situation with two overlapping genes in Cluster J phage NihilNomen which looks like it might be a translational frameshift.

Gene 123 in forward frame 2 is called by Glimmer and GeneMark, albeit both call it short. However, there is an even longer ORF in frame 1 that is called by the host-trained GeneMark.hmm that has very strong coding potential and full overlaps with gene 123 (se attached figure).

Interestingly, the coding potential for the ORF in frame 1 and gene 123 do not overlap: The coding potential for gene 123 starts right where the coding potential for the ORF in frame 1 ends (see attached figure). Furthermore, the coding potential map seems to indicate there is a translational frameshift. The ORF in frame 1 has BLAST matches to phage Thibaut, while gene 123 has matches to phages Omega and Porcelain. In terms of function, both genes have matches to DNA cytosine methyltransferase.

I am unsure what to do here? Call both genes? If so, what to do about the potential translational frameshift? Or should I call only one gene, and if so which one?
Posted in: Frameshifts and IntronsPossible translational frameshift in Cluster J
| posted 12 Feb, 2018 19:27
We have found 4 ORFs located in coding gaps that have significant BLAST matches (<E-10) to other Mycobacterium smegmatis phage genes, but without any coding potential. To call or not to call?
The BLAST matches are as follows:

ORF 1:
gp57 in Mycobcterium phage Send513 with E-value = E-38
gp57 in Mycobcterium phage Papyrus with E-value = E-38

ORF 2:
Many matches to HNH endonucleases in many Mycobacterium phages, all with E-value 0

ORF 3:
gp90 in Mycobacterium phage Send 513 with E-value = E-13

ORF 4:
gp72 in Mycobacterium phage Squirty with E-value = E-27
gp49 in Mycobacterium phage Shuna with E-value = E-21

Thanks for any insight.
Posted in: Gene or not a GeneORFs with BLAST match but without coding potential
| posted 27 Jan, 2018 01:31
Is there a cutoff value of the SD score for start codons, i.e. a value below which you would eliminate a start codon from consideration? I use Kibler6 and Karlin medium per the DNA Master guide.

Posted in: Choosing Start SitesSD scoring matrix
| posted 26 Jan, 2018 21:27
One of our phages, Riparian, has circularly permuted genome ends, and there is a gene that straddles the genome ends (see attached dnam5 file). Can we proceed with annotation normally, or is this going to be a problem later on?

Reply from Deborah Jacobs-Sera:
When you have a circularly permuted genome (that is – a genome without defined ends) we cut it in a gap upstream of the terminase. I cut Riparian according to those guidelines. Sometimes small genes are called that we cannot support with sufficient data. That wrap-around gene is one such gene. Also note that I cut the genome so that gene 1 starts on bp1. So the start of the first gene should be bp 1!

I double-checked my decision of where best to cut this genome and am sticking with it. I do not believe that wrap-around gene is real when you check out the overlap with gene 1.
Posted in: Choosing Start SitesHow to choose the start of the first gene for a circularly permuted genome