[maker-devel] prokaryotic genome annotation

[Panos Sapou]

Dear all

I recently started using maker for the annotation of my prokaryotic genomes
and even if i managed to get some nice results I would like to check with
you if what I did was right and also ask you a couple of questions about
the procedure

I also apologize in advance if I ask sth silly since I am a newbie in
bionformatics and I might ask very basic stuff


I have only available DNA sequences, I have no ESTs and no proteins

1) I started by using the protein2genome option and as reference I used the
Uniref50 database. Then I generated a merged gff file (similar procedure
like the one in the tutorial maker)

2) I used Genemark.S and I created a model by using the gmsn.pl command and
as input the assembled contigs of my bacteria

3) after finishing the above 2 steps I run maker again by using as input
the gff file from step 1: #-------Re-annotation using maker derived GFF3:
maker_gff=input.gff
and I also set
protein_pass=1
is that correct? do you think it helps?
and at the #-----gene prediction I used the hmm.mod file generated in step
2

my questions:
Do the above sound correct?

it is in my understanding that I can only use genemark for prokaryotic
genomes, is that correct?

when I run maker the second time (step 3) should I set protein2genome=1 or
0? or just having the gff file (from step 1) in the re-annotation options
is enough? and thefore prediction based on the protein2genome has already
been done?

Also if I use a gff file (from step 1) will it make any difference if I set
protein2genome=1 and use an extra (different) database? (I was wondering if
it will improve the results?)

finally regarding the choice of the database: would you advise me to use
uniref or the proteomes of closely related bacteria (I have downloaded and
created a single fasta from appx 100 proteomes of closely related bacteria)

thank you in advance
and once again I apologize if it is pretty basic what I am asking, just
wanted to make sure...


Best
Panos
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