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kmaclea posted in RefSeq and INSDC name disagreements in NCBI Blast for Functonal Assignment

cdshaffer posted in RecA in cluster BN

Allison Johnson posted in anti-CBASS type III-C protein

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Debbie Jacobs-Sera posted in anti-CBASS type III-C protein

All posts created by grosasacosta

| posted 13 Feb, 2020 18:47
grosasacosta avatar
grosasacosta
Thank you so much, Welkin! I knew Catalina was going to bring issues, I guess that's what happens when you can't use WINE…smile
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| posted 12 Feb, 2020 22:46
grosasacosta avatar
grosasacosta
Some of the students in my class that use Macs are having issues installing DNA Master. Is there any known compatibility issue with Catalina? It seems like the ones that are not having any issues are the ones who didn't upgrade to Catalina. Please let me know.
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| posted 12 Jun, 2018 14:32
grosasacosta avatar
grosasacosta
Sounds good, Dan. Please let me know as soon as you get to it. THANKS!!!
Posted in: Frameshifts and Introns → New frameshift in an A1 phage?
| posted 12 Jun, 2018 02:04
grosasacosta avatar
grosasacosta
Welkin Pope
We have no wet bench data for any frameshifts in anything other than the tail assembly chaperones. So while this is cool, we are not going to annotation this with a frameshift between the two pieces.
Totally understandable, Welkin. So, should I assign the same function to both genes?
Posted in: Frameshifts and Introns → New frameshift in an A1 phage?
| posted 11 Jun, 2018 20:29
grosasacosta avatar
grosasacosta
For phages in Cluster A, Tail assembly chaperons are the only type of genes accepted to contain frameshifts. However, while annotating Anglerfish (an A1 subcluster phage), gp13 and gp14 appear to be identical to the N- and C-terminal half regions of capsid maturation protease, respectively. I have searched for slippery sequences and have not found perfect matches, although did find the GGGAGA sequence (very similar to GGGAAA) in the overlapping region. What should be done about this? A BLASTN analysis of this region shows a one-nucleotide difference with Dreamboat on the sequence GGGCGC (this sequence reads GGGCTC in Dreamboat), and this difference is also within the region where the two sequences overlap.
Posted in: Frameshifts and Introns → New frameshift in an A1 phage?
| posted 12 Feb, 2018 22:25
grosasacosta avatar
grosasacosta
I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting.
Posted in: Gene or not a Gene → ORFs with BLAST match but without coding potential