Hi,
I heard there was 3 good annotation pipelines for genome annotation.
1) Maker - Need access to rep base (proprietary)
2) Braker - open source
3) Augustus - open source
According to the manual Braker pipeline only uses translation_table = 1 only for Eukaryotes.
Augustus supports different translation_table
For fish genomes annotation which one need to be used translation_table = 1 or 2
Suggestions please.
Selection analysis -
Using codeml I performed a test run on only one ortholog
Selected codontable 2 (Vertebrate mitochondrial code) in pal2nal.pl
Do I have to select codontable 1 (fish genomes) ?
**-codontable N**
1 Universal code (default)
2 Vertebrate mitochondrial code
pal2nal.pl OG0018563.mt.r.fa all_OG0018563.fa.fa -codontable 2 -output paml > all.log
#------------------------------------------------------------------------#
# Input files: OG0018563.mt.r.fa all_OG0018563.fa.fa
# Codontable 2 is used
# WARNING: A.ve pepAlnPos 114: R does not correspond to AGG
# WARNING: A.ve pepAlnPos 120: R does not correspond to AGG
# WARNING: A.ve pepAlnPos 121: R does not correspond to AGA
# WARNING: A.ve pepAlnPos 172: R does not correspond to AGG
# WARNING: A.ve pepAlnPos 251: R does not correspond to AGA
# WARNING: C.lu pepAlnPos 14: R does not correspond to AGG
# WARNING: C.lu pepAlnPos 15: R does not correspond to AGA
# WARNING: C.lu pepAlnPos 58: R does not correspond to AGA
# WARNING: C.lu pepAlnPos 114: R does not correspond to AGG
# WARNING: C.lu pepAlnPos 120: R does not correspond to AGG
# WARNING: C.lu pepAlnPos 121: R does not correspond to AGA
# WARNING: C.lu pepAlnPos 172: R does not correspond to AGG
# WARNING: C.lu pepAlnPos 228: R does not correspond to AGG
# WARNING: C.lu pepAlnPos 251: R does not correspond to AGA
The NCBI table refers to mitochondrial genetic codes mostly.
You can use MOSGA to figure out the best predictions, including BRAKER(2), Augustus, GeneMark, SNAP and functional annotation.
Can't we run MOSGA, with out docker, to be honest I don't like docker.
Our servers doesn't have access to docker, my admin wont allow to install it.
Suggestions please.
we are currently working on a Singularity implementation, but you can always run on the demonstration server (with a waiting queue)
Alternatively, you can install a VirtualBox with ubuntu 20.04 and run the Linux installation guide.
MOSGA does not have to run necessarily on a server, it works fine on my Notebook or Desktop.
Can we run as a standalone version similar like braker.pl ?
No, MOSGA contains over 60 software, a web server and 60 GiB databases.
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