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All posts created by welkin

| posted 15 Aug, 2018 17:45
These six G1 phages were reviewed collectively by Welkin on Aug 15 2018:

Posted in: Cluster G Annotation TipsRecently reviewed genomes
| posted 13 Aug, 2018 18:03
The integration cassette– integrase, immunity repressor, and excise – are well-characterized in BPs, including function and confirmed start sites.
See Broussard et al
Posted in: Cluster G Annotation Tipsintegration cassette
| posted 07 Aug, 2018 16:45
Please take a look at this thread:
Posted in: Cluster BH Annotation Tipstail assembly chaperones in BH?
| posted 07 Aug, 2018 16:44
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.
Posted in: Functional Annotationtail chaperones in cluster BH
| posted 07 Aug, 2018 16:16
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.
Edited 07 Aug, 2018 16:17
Posted in: Request a new function on the SEA-PHAGES official listelongation factor P
| posted 07 Aug, 2018 16:03
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.

Posted in: Functional Annotationtail chaperones in cluster BH
| posted 20 Jul, 2018 15:31
Posted in: Request a new function on the SEA-PHAGES official listAcetyltransferase
| posted 19 Jul, 2018 16:36
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.

Edited 19 Jul, 2018 16:36
Posted in: DNA MasterOdd BLAST results via DNAMaster
| posted 19 Jul, 2018 12:37
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:

Posted in: DNA MasterRunning DNA Master on a Mac using Wine
| posted 17 Jul, 2018 16:22
Thanks for sharing— I agree, that is a nice way of noting things.
Posted in: Notes and Final FilesSuggested Format for Documenting Synteny