Kenji Fukushima

I just tried it and got no hits in the RCSB advanced search.

No hits seem to be a valid result, and it's not treated as an error in the RCSB's advanced search. Since this is expected behavior in GUI, it might be...

I am still wondering how I should handle this error. Any suggestions are appreciated.

I'm sorry I missed your reply. As a workaround, I'd like to handle it with try-except for now. If I get a chance to learn more about pypdb’s code in...

I don't have the RepBase subscription but RepeatMasker is still useful because the latest version comes with the out-of-the-box Dfam repeat database (see [here](http://www.repeatmasker.org/RepeatMasker/)), so Repbase is no longer necessary....

RepeatMasker seems to automatically download the latest Dfam release, which is currently 3.3 and contains 347 species, although I don't know how many fungal species there are. ``` (funannotate) [kfuku@at137...

I got the same error with my dataset. In my case, lowercase letters (atgc, instead of ATGC) seem to have caused the problem, and it was solved with the input...

With my dataset, I got a new error that might be coming from `split_large_gf.pl`, which was probably not used for the test dataset. ``` Invalid command line Unknown option maxiters...

WGDdetector successfully completed analyzing some plant genomes with the above modification.

I analyzed 20 species and only in 1 species I got the error reported in #7 . Because the failed input file used `atgc` instead of `ATGC` to code nucleotide...