jrr-cpt
commented
4 years ago @ltmaddox Call the directory: advanced-lysis-genes Title: Advanced Lysis Gene Search
Description: This tutorial expands on what has been discussed in the (link to first lysis gene tutorial). When lysis genes were not identified by inspection of Functional Workflow outputs, try some of the tools described below.
Agenda:
- Tools for finding spanins
- Tools for finding holins
- Tools for finding endolysins
- Tools for checking the proximity of potential lysis genes
A reminder: Bioinformatic tools cannot always be used to identify novel lysis genes. A conservative approach is preferred to calling something a lysis gene when it isn't, but researchers should still do their due diligence before concluding that their phage's lysis genes are not identifiable with the tools/databases in their current state.
Tools for finding spanins: Brief para on spanin features, and what functional workflow looks for.
Link to and describe ISP/OSP/Find Spanin tools, and the workflow that chains them together. Show example output. Describe how gff3 can be piped to Apollo.
Also link to LipoP (and lipoP to gff) and Lipobox.
Tools for finding holins Brief description of holin types.
Link to TMHMM tools (there are two, one makes graphs and the other the gff3 that usually goes to Apollo), and the search file tool (tell them to check the holin/antiholin boxes, search through the blast results and interpro results).
Tools for endolysin Search file tool (tell them to check the endolysin boxes, search through the blast results and interpro results).
Proximity Discuss cassettes, which doesn't apply to some larger phages. Leave space to describe prox to lysis concept. Link to AMH new tools. In reality this can be a Coming Soon section for now, since these tools aren't all finished.
In the cases where the lysis genes were not found through the structural workflow, there are a few tools in Galaxy specifically to address something that may have been missed.
-Primarily, this can detail how to use the isp/osp/Find Spanin tool suite (and possible workflow).