Link to this post | posted 15 Aug, 2018 17:45
welkin	These six G1 phages were reviewed collectively by Welkin on Aug 15 2018: Paito Grizzly Sweets Hotshotbaby7 Kasen3 Olga

Link to this post | posted 13 Aug, 2018 18:03
welkin	The integration cassette– integrase, immunity repressor, and excise – are well-characterized in BPs, including function and confirmed start sites. See Broussard et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557535/#SD1

Link to this post | posted 07 Aug, 2018 16:45
welkin	Please take a look at this thread: https://seaphages.org/forums/topic/4760/?page=1#post-6634

Link to this post | posted 07 Aug, 2018 16:44
welkin	ok. Then I think for now, I will link this thread to the Cluster specific forum for BH– that should help with all future annotations. I am sorry I can't give you a clearer timeline for the ones that are currently in.

Link to this post | posted 07 Aug, 2018 16:16

welkin

so in this particular case, the Saguaro gene is not long enough to be a full EF-P. It should be around 180aa, and this is only 107. EF-P was crystallized in sections, and this appears to be aligning to the OB domain, which is a beta-barrel. We might add elongation factor P to the functional list at some point, but I don't think this gene has enough evidence. http://www.pnas.org/content/101/26/9595.long Edited 07 Aug, 2018 16:17

Link to this post | posted 07 Aug, 2018 16:03

welkin

So this is a multi-part question: one, the logistics, and two, the timeline. logistically, changing a file means submitting a five-column feature table that contains all the features and locus tags of the current records, only with the edits you would like. once you have this file and have edited it, we can send it to GenBank and request an update to the record. A caveat to that would be for records that have not yet gone live; in that case, we could probably make a new asn1 file and ask to replace the older asn1 file with the new one. timeline wise—At the moment, we'd prefer that you let us submit all the changes to the files in GenBank– the staff has requested that we not try to change the same file too many times in a row (they'd prefer a single file with all updates if possible). As we are in the middle of trying to reconcile a lot of genomes right now it would probably not be great for you to send them something and then me to send them something else the next week. so if you would like to collect all the current files and adit them and make the five column tables, I can take a look, and submit the changes along with any others we've got for these. Welkin

Link to this post | posted 20 Jul, 2018 15:31
welkin	approved!

Link to this post | posted 19 Jul, 2018 16:36
welkin	Hi Jim, Those strings of Xs are the result of a low-complexity sequence filter that BLAST has which is enabled in DNA Master. Unfortunately, there is no way to turn it off in the program, but you can redo the search on the NCBI website with the filter off if you want. Best, Welkin Edited 19 Jul, 2018 16:36

Link to this post | posted 19 Jul, 2018 12:37
welkin	Please note— this thread was too long and covered too many different topics over a number of years, so we have closed it and restarted it as a separate forum under DNA Master. please start new threads here: https://seaphages.org/forums/forum/160/ Thanks! Welkin

Link to this post | posted 17 Jul, 2018 16:22
welkin	Thanks for sharing— I agree, that is a nice way of noting things.