Link to this post | posted 15 May, 2018 15:11
welkin	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

Link to this post | posted 12 May, 2018 13:40
welkin	Are you using the HTTPS setting to connect to NCBI? Have you tried the same file on a different computer?

Link to this post | posted 12 May, 2018 13:39
welkin	Hi Joe, Did you also tell it to reassign gene names and products when you renumbered the locus tags?

Link to this post | posted 11 May, 2018 15:31
welkin	Great! Check the override box to the right of the locus tag field and you should be able to enter the underscore.

Link to this post | posted 11 May, 2018 12:26
welkin	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

Link to this post | posted 11 May, 2018 12:25
welkin	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!

Link to this post | posted 09 May, 2018 12:01

welkin

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

Link to this post | posted 08 May, 2018 14:43

welkin

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. Thanks! Welkin

Link to this post | posted 07 May, 2018 16:49
welkin	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.

Link to this post | posted 03 May, 2018 20:05

welkin

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. Thanks! Welkin