[Gmod-ajax] Apollo / JBrowse2 & other tools for genome annotation?

[Timothy F. <tf...@uc...>]

Hello Apollo <https://github.com/GMOD/Apollo> users (and CCed JBrowse2 user list),

I tried Apollo some years ago, but it didn’t quite work for my genome annotation problem (my memory is a little fuzzy as to why it didn’t work out). 

I’d like to give it another shot, but have a couple questions that I think your respective user communities might have insight into:

1. Does Apollo’s graphical editing of gene models have a mode where it biologically constrains the edits? E.g. exon-intron splice junctions can only be dragged to another valid slide junction (based the AG/GT sites), or start codons can only be dragged to other ATGs (in other words, these features would “snap” to coordinates that have compatible sequences with their biological function)

2. Does anyone have a favored strategy or suite of tools for manual or semi-automated gene family annotation?  In my past work, I came down on the “mostly-manual” side of things - looking at blast alignments in a genome browser, manually editing the GFF file with nano, and regenerating the translated peptides from the GFF to make sure I didn’t muck up the splicing or frame, while tracking it all with git to ensure I had a sort of “audit log” for these changes as I did them on-and-off over a few weeks. You can actually see the history of that here: https://github.com/photocyte/PPYR_OGS/commits/master <https://github.com/photocyte/PPYR_OGS/commits/master> . 

I’m sure there must be a better way to do things (and Apollo may be it!) but I hadn’t quite figured it out yet. I greatly appreciate any guidance you can provide.

All the best,
-Tim
___________________________________
Timothy R. Fallon, PhD
NIH NRSA Postdoctoral Fellow - Moore Laboratory

Center for Marine Biotechnology and Biomedicine 
Scripps Institution of Oceanography 
University of California, San Diego 

tf...@uc...
Google Scholar publications and citations <https://scholar.google.com/citations?hl=en&user=CEPlauQAAAAJ&view_op=list_works&sortby=pubdate>
Website: http://photocyte.github.io <http://photocyte.github.io/>