Eric Nawrocki

Looks like that is a chicken lncRNA sequence being aligned to a plasmodium RNase P model, so the resulting structure wouldn't be biologically meaningful. @davidhoksza : The segfault is probably...

Okay, so sounds like another option for traveler might be to detect if cmalign fails with this error and exit cleanly, but I'm not sure how hard that is to...

I tried to reproduce these two secondary structure diagrams with a local installation of R2DT, and was able to for URS00021ED94B but my structure for URS000075D341 is different than what...

@AntonPetrov and @janstrauss1 : the `esl-construct` program installed with HMMER or Infernal (http://eddylab.org/infernal/) using the -x option can make a consensus structure from individual secondary structures but you'd need the...

@janstrauss1 are you able to export the sequences with gaps as an alignment? It looks to me like the example text file you provided is not an alignment (unless they...

@janstrauss1 - thanks! I should be able to look into this next week.

Hi @janstrauss1 I wrote a simple perl script that converts your ITS2db_prasinophytes_example_alignment.txt file to Stockholm format with individual sequence SS annotation and attached it here. [its2-to-stk.pl.txt](https://github.com/RNAcentral/R2DT/files/6928027/its2-to-stk.pl.txt) (Note that I had...