How to run GeneMark for detection of frameshifted genes

Question

[konstantinkul]

Hi all!

Does anybody know how to run GeneMark on a prokaryotic genome to detect possibly frameshifted genes in the report? I will be grateful for a specific list of commands with short explanations.

Thank you

[Joe]

From what I can see in their documentation, it claims that GeneMark is capable of identifying frameshifts. There is not option that specifically seems to enable/disable this behaviour, so as far as I can work out, its presumably active at all times, and running the software should just predict them.

Have you tried it and encountered some issue?

Others might know better than me, but I can’t see anything obvious you need to do specifically.

[konstantinkul]

In readme file developers discribe genemark suite

one of the version include this option

GeneMark version 2.5m    -g {0,k,n,o,r,s,x,l}
      0: Don't produce graphic output (clear flags/defaults)
      k: Use alternative scale for graph
      n: Mark stop codons on graph
      o: Mark open reading frames on graph
      r: Mark regions on graph
      s: Mark start codons on graph
      x: Mark putative exon splice sites
      l: Print graph landscape
      **f: Mark putative frameshift errors**

But I have no idea how they run this command especially where I can find the parameter file (-m) and RBS model (-R)

   -m <filename>
      Name of parameter matrix file to use
   -R <filename>
      Name of the RBS model file to use

[konstantinkul]

I found that web-service http://exon.gatech.edu/GeneMark/gm.cgi allow detecting frameshifts, but they use an old version of GeneMarkS 4.25

[Joe]

Do you have a link to that specific documentation?

[konstantinkul]

The last news, I contacted developers and they answered my questions. Ivan Antonov said that I had to use the GeneTack tool

You can run GeneTack using pre-built models (prokaryotic or eukaryotic) on a web-server: http://83.149.211.146:23194/~ivan/cgi-bin/GeneTack/cgi/genetack.cgi http://83.149.211.146:23194/~ivan/cgi-bin/GeneTack/cgi/genetack_euk.cgi

Or install it locally from: https://sourceforge.net/projects/genetack/