Translation table for annotating fish genomes ?

Question

[sunnykevin97]

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

Augustus manual

The genetic codes

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

Answer 1

[BioinformaticBird]

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.

[sunnykevin97]

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.

[BioinformaticBird]

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.

[sunnykevin97]

Can we run as a standalone version similar like braker.pl ?

[BioinformaticBird]

No, MOSGA contains over 60 software, a web server and 60 GiB databases.

[sunnykevin97]

braker issues

Braker and Augustus refering to the translation table 1

Vertebrates are table 1.