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All posts created by welkin

| 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.


Best,
Welkin
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:
https://seaphages.org/forums/forum/160/

Thanks!
Welkin
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
| posted 17 Jul, 2018 16:18
no, we are not calling those three small proteins minor tail proteins any longer. Only the lengthy ones.

thanks!
Posted in: Functional Annotationminor tail proteins in A1s
| posted 17 Jul, 2018 16:03
Hi Maria,
I think you can use terminase small subunit here.
Thanks!
Posted in: Functional AnnotationCluster K5 terminases
| posted 17 Jul, 2018 16:01
This one has me stumped– it hits the trifecta of things I don't like to put in official function names: a TLA, a structural motif, and a phenotype.

I really dislike TLAs in the functional annotations, unless it is one like "DNA" which is totally unambiguous and everyone knows. You are right that DPS is simplistic and uninformative.

re the ferritin component— is it actually binding iron? I dislike naming functions after the structural fold of something that does something completely different—

And DNA protection during starvation could be accomplished by a number of proteins with different shapes.
Thoughts?
Posted in: Request a new function on the SEA-PHAGES official listDPS protein for Yaboi_draft 37
| posted 17 Jul, 2018 15:55
Hi Maria,
It is always worth asking Becky and Dan to double-check the sequence when you find a disruption in a gene with a known function. We do find errors in sequences, especially those that were sequenced with the Ion Torrent technology. It is pretty rare in those sequenced with Illumina.

If the sequence is legitimate, you could annotate it is RtcB-like ligase, truncated. As you noted, we don't add frameshifts to the annotations, other than for the tail assembly chaperones.
Posted in: Frameshifts and IntronsNew Frameshift in K5 bacteriophage RtcB-ligase ?
| posted 05 Jul, 2018 20:16
I agree. Sounds like some revisions I need to make in those revisions. Thanks!
Posted in: Functional Annotationholin with zero transmembrane domains in F cluster phage?
| posted 05 Jul, 2018 20:14
Hi Sarah,
How similar is it to MPME1? And does it have the rest of the MPME features? If so, it sounds like you may have MPME 3….
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 05 Jul, 2018 20:13
Sold!
Posted in: Request a new function on the SEA-PHAGES official listjustbecause 252 @ 149782 "ADP-ribosyltransferase"