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All posts created by welkin

| posted 25 May, 2018 14:53
Hi Ken,
Either is fine. The computer program will truncate whatever you put in the "first name" column down to a single initial.

Thanks for asking.
Welkin
Posted in: Notes and Final FilesAuthors file
| posted 23 May, 2018 13:28
Hi MArie,
Do you have any BLAST results for lysins in the Mycobacteriophages? The lysin A domains were extensively characterized by Kim Payne in Graham's lab.
My favorite way to assign the domains is to align the gordonia lysins with the phages from the Payne and Hatfull paper in 2012 about lysins. Kim really did that bench work, so if you have sequence alignment to those domains, you can feel confident about being more specific.

Thanks!
Posted in: Functional AnnotationLysins in Gordonia
| posted 22 May, 2018 15:34
Hi Nikki,
You are right— one amino acid off means we will stay with MPME1.

Thanks!
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 15 May, 2018 15:11
Hi All,
We consider "gene 1" to be the gene with the lowest start coordinate.

sometimes the computer programs will reorder the list of genes to put the gene that contains the lowest coordinate at the top of the list.
thus, the last wrap-around gene is gene 258 (or whatever) is at the top because it contains bp 1. Gene 1 starts at bp 15.

hope that helps.

Welkin
Posted in: Choosing Start SitesHow to choose the start of the first gene for a circularly permuted genome
| posted 12 May, 2018 13:40
Are you using the HTTPS setting to connect to NCBI? Have you tried the same file on a different computer?
Posted in: DNA MasterDNAMaster BLAST failure
| posted 12 May, 2018 13:39
Hi Joe,
Did you also tell it to reassign gene names and products when you renumbered the locus tags?
Posted in: DNA MasterFInal gene order renumbering issue
| posted 11 May, 2018 15:31
Great!
Check the override box to the right of the locus tag field and you should be able to enter the underscore.
Posted in: DNA MasterDNAMaster BLAST failure
| posted 11 May, 2018 12:26
Hi Tammy,
I have never seen that error before. I recommend trying a partial batch BLAST– 10 to 20 genes or so at a time, and then saving after each successful one.

Good luck!
Welkin
Posted in: DNA MasterDNAMaster BLAST failure
| posted 11 May, 2018 12:25
Hi Joe,
As long as the BLAST data matches the start chosen in the file, you are all set– no need to reBLAST.
Thanks for checking!
Posted in: How to Pass Preliminary Annotation ReviewRe-BLAST final dnam5 file
| posted 09 May, 2018 12:01
Hi Amanda,
These are in the new online Bioinformatics Guide.
Information about Synteny
https://seaphagesbioinformatics.helpdocsonline.com/article-90
https://seaphagesbioinformatics.helpdocsonline.com/officialdocumentation

Information about Starterator:
https://seaphagesbioinformatics.helpdocsonline.com/article-37
https://seaphagesbioinformatics.helpdocsonline.com/officialdocumentation

Please note, we are no longer recommending or updating the DNA Master Annotation guide. All of the latest information will be in the Online guide.

Best,
Welkin
Posted in: PECAANSynteny + Starterator Fields