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All posts created by welkin

| 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.

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
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!
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

Information about Starterator:

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.

Posted in: PECAANSynteny + Starterator Fields
| posted 08 May, 2018 14:43
Hi Megan,
These are certainly minor tail proteins. Some minor tail proteins have enzymatic activity, it can helps the phage recognize the correct host, get through the cell surface, and/or through the cell wall to inject the DNA.
The most compelling evidence is synteny– the phage needs a certain number of minor tail proteins to make a tail. This gene is the right size and in the right place, and it is too big to be a lysin domain.

Posted in: Functional AnnotationMinor Tail Protein (Pham 21676) in EA Phages?
| posted 07 May, 2018 16:49
The integrase in the AS phages is usually missed by the gene calling programs and four incorrect genes are predicted in the opposite strand in the same region.
Posted in: Cluster AS Annotation Tipsintegrase
| posted 03 May, 2018 20:05
Hi Tammy.

1. STarterator is informative if there is more than one other pham members. It doesn't matter if the phams have a known function or if the genomes still have draft annotations. The point is to see if the starts are conserved throughout the group.

2.for the synteny note, you should be looking at the gene content of your own genome. Does the terminase fall in the left arm of the genome and is it followed by the portal? Finding other genomes to reference can be helpful but is not essential.

3. you don't need to list all the hits but it would be good to indicate that all the analyses were run.

4. you check the box labeled "override" that is to the right of the locus tag box in the validation tab.

Posted in: Notes and Final FilesAnnotation check questions