Yasuhiro Tanizawa

How about installing BioPerl using conda ``` conda install -c bioconda perl-bioperl ``` https://anaconda.org/bioconda/perl-bioperl

I tried to install prokka to a clean conda environment on Mac, but I got the same error. ``` Can't locate Bio/Root/Version.pm in @INC ... ``` I found a similar...

Fragmentation of the IpxA gene might be correct in this case. Here you can see the original annotation of NZ_CP006571.1, https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP006571.1 It is annotated as peudogene because of the frameshift...

Currently, there is no option for that. I will make it available in the next update. Thank you for the comment.

Dear Dieter @aistBMRG Thank you for using DFAST. I saw this kind of error for the first time. Probably it was raised while running "makeblastdb" command. Please check it by...

Thank you for trying DFAST, @Rui-Zzhang Since DFAST web service moved to a new server in February 2021, the URL in the v1.2.12 is no longer accessible. To avoid the...

Yes. It detects internal stop codons and frameshift. Please see the note tags in GFF or GenBank format. ``` /note="Partial hit; WP_003643223.1 gluconate permease (Lactobacillus plantarum WCFS1) [pid:71.3%, q_cov:100.0%, s_cov:44.8%,...

Please check the log file (application.log) for the number of pseudogenes. It says as following: ``` 2020/11/06 21:04:09 6 CDS features were marked as possible pseudo due to internal stop...

@ireneortega Well, currently there's no straightforward way to do that. I would write a script to parse a .gbk file and extract such location.

@nick-youngblut @ireneortega @vappiah As of ver.1.2.15, DFAST generates the summary file for pseudogenes. Here is an example: https://dfast.ddbj.nig.ac.jp/analysis/download/54a8ce11-3b1c-4ccb-8644-b316c7c60bf9/pseudogene_summary.tsv (not a parmanent link, will be deleted in a month) Please have...