Diogenes
Muse
- Joined
- Oct 5, 2012
- Messages
- 978
So I'm looking for a better tool to assess potential transcription factors along a 19 MB genome. One is gal4-like and the other is a GATA-type.
I can't assume obligate homodimerization (afaik) as I don't have good homology past the respective zinc fingers.
What I'm currently using is Geneious R6, I've automatically annotated potential sites (Went with CCG-N10-GGC for the gal4-like as N11 had no matches and A/T-GATA-A/G for the gata-like).
I'm running these as inverse, too, which might not be correct, I suppose, though since these are cis-acting my guess is that genes transcribed in the "opposite" direction would have a correspondingly inverted UAS.
I'm manually going through the genome where there are hits (just ctrl+finding) and if there is one hit upstream of a gene within 1 kb I write that down and I note the number of binding sites. I'll likely leave all the single hits alone and just focus on proximate multiple hits. I also reject binding sites within coding regions for the time being.
This actually won't take forever, I'm just wondering if there's an easier way.
I can't assume obligate homodimerization (afaik) as I don't have good homology past the respective zinc fingers.
What I'm currently using is Geneious R6, I've automatically annotated potential sites (Went with CCG-N10-GGC for the gal4-like as N11 had no matches and A/T-GATA-A/G for the gata-like).
I'm running these as inverse, too, which might not be correct, I suppose, though since these are cis-acting my guess is that genes transcribed in the "opposite" direction would have a correspondingly inverted UAS.
I'm manually going through the genome where there are hits (just ctrl+finding) and if there is one hit upstream of a gene within 1 kb I write that down and I note the number of binding sites. I'll likely leave all the single hits alone and just focus on proximate multiple hits. I also reject binding sites within coding regions for the time being.
This actually won't take forever, I'm just wondering if there's an easier way.
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