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All posts created by welkin

| posted 15 Sep, 2016 18:20
The DNA primase of the cluster A phages is split into two overlapping reading frames. The upstream portion of the gene is frequently missed by Glimmer and Genemark. 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 A Annotation TipsDNA Primase
| posted 01 Sep, 2016 14:25
Hi Chris,
I just tried to do new installs of BetaStarterator and failed miserably. The terminal seems to go through removing all the appropriate items, clones stuff, resolves stuff, and switches to a new branch "Beta"
lists a few file lines
/home/seafaculty/Applications/Starterator/starterator/starterator.sh
/home/seafaculty/Applications/Starterator/starterator
Already up to date.
starterator.sh: line 10: //home/seafaculty/Applications/Starterator/starterator/Starterator: no such file or directory
?

lots more errors.

IT looks to me like there was an accidental capitalization of the word Starterator in the most sub directory in the script in line 10. Maybe?

help…
Posted in: StarteratorStarterator Updates available for beta testing
| posted 25 Aug, 2016 20:56
Hello All,
Some faculty are reporting clumping in their Gordonia liquid cultures. Here are some ways to get rid of clumps.

Ways to get rid of clumps:
You can use Tween, like smeg in starter cultures, and then transfer to larger ones.
You can start with a small liquid culture and then use it to innoculate a larger one. Using a higher OD culture can help, because you can let any initial clumps settle to the bottom and just innoculate using cells from the top.

Make sure you don't grab a big chunky colony (or clump) and use it as part of your innoculum.

Clumping is actually so bad in some other Gordonias that they have to be sonicated prior to plating so we can get decent lawns.

-Welkin
Posted in: GordoniaClumping in liquid cultures
| posted 26 Jul, 2016 18:12
I love the gray vs red, and the shading to indicate conservation. IT is really nice.


pham 10201 is almost impossible to read no matter what the colors look that. Too many starts! I am not sure how to fix that. I am finding myself wishing for a Zoom function. Is there anyway to say " OK, I just want to see the first 50 amino acids, redraw?"


I am also having trouble reading the start numbers with the large font– too many of them are on top of each other and on the tracks. Maybe space the tracks farther apart and bump the numbers up outside the tracks?
-Welkin
Edited 26 Jul, 2016 18:18
Posted in: StarteratorStarterator UI updates
| posted 27 Apr, 2016 14:01
In general, we have been trying to move away from using three letter abbreviations in the majority our functional assignments, so please don't use 'SAP domain'.
If you have good evidence for a function that is not on the approved list, please feel free to assign a gene that function, just make sure you write it out clearly.
However, please make a note of it in your cover sheet for the annotation, so SMART can take a careful look and decide if it should get added to next year's approved list.

Thanks for the question!
Welkin
Posted in: Functional AnnotationFunction called for some but not all members of pham
| posted 13 Apr, 2016 19:21
Hi Roy,
What a great question! Do you have HHPred or BLAST results that support the intact catalytic domain of an esterase? If so, go with esterase. Otherwise, more general might be better.

Thanks!
Welkin
Posted in: Functional Annotationhydrolase, esterase or hydrolase/esterase?
| posted 28 Mar, 2016 16:49
Hi Marie,
HNH endonucleases are little parasitic selfish genes that move quickly through the genomic landscape– much more quickly than they would evolve to match phage genome's coding potential (think transposons).
They routinely have poor coding potential in genemark outputs for this reason, but usually have pretty good HHPred alignments because the 3D structure is conserved. Some HNH endonucleases even give false positives in GeneMark– that is, it looks like there is coding potential in the opposite strand. So if you are seeing HNH endonuclease as your functional assignments in phagesdb and phamerator maps, don't worry about poor coding potential.
Posted in: Gene or not a GeneCluster B gene with no coding potential
| posted 03 Mar, 2016 16:23

The final score is what determines which you should rate "best". However, I would think there would be few, if any, cases where the final score (based on match to matrix and length from start codon) and Z -value (standard deviation from random sequence) don't both point to the same start. Was your example from your genome or a hypothetical?

Welkin
Posted in: Notes and Final FilesSD Scoring in notes
| posted 26 Feb, 2016 20:22
Hi Joy,
It just means that you need to streak out the potential lysogens for single colonies. Here is a youtube video (tps://www.youtube.com/watch?v=Ay2hhujTuvg)
You can use sterile wooden sticks, an innoculation loop, sterile toothpicks, etc. I like sticks for students, they are easier to use and tend not to accidentally gouge into the agar surface as much.

The streaking serves two purposes: one, to grow up a single clonal colony to work from, and two, to remove any exogenous phage that might be left over from the initial mesa spot. Sometimes you can get a mix of resistant cells and true lysogens. Streaking to purify cells and then working from a purified clone is good microbiology practice.
Posted in: Lysogeny/ImmunityLysogeny experiment help
| posted 24 Feb, 2016 15:45
So question 1: is it the DNA primase? All the primases are split into two overlapping reading frames in the Cluster As. We are trying to figure out how this works biologically (frameshift? splice?) but don't know yet. If it is not the primase, please send us the sequence coordinates so we can make sure it isn't a sequencing error.
Question 2: if the immunity repressor gets inactivated through mutation, you will no longer have a temperate phage (or be able to form a lysogen in the first place). If the phage integrates and THEN somehow the repressor got inactivated, the prophage would still come out. so either way, there would not be a lysogen around to test. To answer the other part of your question, if you had an A6 prophage, and infected that lysogen with an A1 phage (that has a different recognition sequence for the immunity repressor), yes, you would make plaques on the lysogen.
Posted in: Lysogeny/ImmunityOne of our draft phage genomes has a 'stop' in the middle of the immunity repressor gene.