Andreas Leimbach

If you don't want Prokka to rename your contig SeqIDs don't set `--compliant` and `--centre`, see issue #141. However, if your SeqIDs are too long you cannot get "correct" Genbank...

Hi Janet, this doesn't solve the possible bug, but there might be another Bioperl way. The DEFINITION line also includes the "segment" statement. Thus, you might skip those entries e.g....

I agree only using `contig000001` or even shorter `c000001` would be a workaround for this issue. Actually the whole problem lies with NCBI's `tbl2asn` which is very strict with its...

Hi @jvollme, thanks for bringing up the issue! 1. Windows Unix line ending issues are very annoying, that's why I recommend running `dos2unix` on the files https://github.com/aleimba/bac-genomics-scripts#windows---unix-linebreak-problems. And of course...

Hi @sirmicrobe, I'm glad `cdd2cog.pl` is useful to you! Well, ahem, planned to do this quite some time ago, never got around to do it. It's quite low priority on...

Hi Alexandre, **Cog** is the preformatted RPS-BLAST+ database that can be found here: ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz You're right that could be clearer in the README. You need to download all the files...

From Alexandre: Thank you for your answer: I ran the command for RPS-blast rpsblast -i c_prot.faa -d /home/lgmmicrorganismo/Programas_Analise/cdd2cog/banco_de_dados/ -o rps-blast.out -evalue 1e-2 -outfmt 6 and got this message: [rpsblast] ERROR:...

try 0.01: rpsblast -query c_prot.faa -db /home/lgmmicrorganismo/Programas_Analise/cdd2cog/banco_de_dados/Cog -out rps-blast.out -evalue 0.01 -outfmt 6 HTH, Andreas

From Alexandre: Ok, just one last question. After running cdd2cog on my protein I got this: Overall assignment statistics: ~ Total query proteins categorized into COGs: 3190 ~ Total COGs...

Hi Alexandre, sorry for replying that late. Unfortunately, the rpsblast is not the most sensitive. However, it's quite weird, that you only have so few functional categories. Normally the number...