Hi again,
I managed to make genbank files in Artemis, and converted the exon
features to CDS, but still I don't see why these are not visible in
the GUI. I ve been comparing with a genbank file that works, and there
are differences in the features under CDS/mRNA, but I would think that
these can be ignored if not present.Unless I miss something, there is
no reason why it should not work.
Ex from my file:
FEATURES Location/Qualifiers
source 1..152837
gene 348..2319
/gene="maker-assembled49-sp-gene-0.84"
mRNA 348..2319
/gene="maker-assembled49-sp-gene-0.84-mRNA-1"
CDS
join
(348
..
606,560
..
606,674
..
749,674
..
749,823
..1370,823..1370,1423..1454,1423..1454,1527..1726,1527..1812,1881..2319)
/codon_start=1
/gene="maker-assembled49-sp-gene-0.84-mRNA-1:CDS:
467"
/score=7669
Ex from the file that works:
FEATURES Location/Qualifiers
source 1..6548
/organism="Neurospora crassa"
/mol_type="genomic DNA"
/db_xref="taxon:5141"
/mating_type="a"
gene <3227..>4485
/gene="m"
mRNA join(<3227..3396,3450..3718,3776..>4485)
/gene="m"
/product="m"
CDS join(3227..3396,3450..3718,3776..4485)
/gene="mt "
/codon_start=1
/product="mm"
/protein_id="X"
/db_xref="GI:1XX"
/translation="somesequence"
I noticed the presence of < in join( in the file that works, but I am
not sure if this is a systematic part of genbank formats.I suspect
this is not the place to ask for genbank formats, but I am not sure
whether there are certain minimum requirements in MAUVE for a format
to be correctely parsed as Genbank. Note that there are no errors in
the console, I just cant visualize the features in the GUI (but I can
see the species name at least)
On 30 Jun 2010, at 23:18, Aaron Darling wrote:
> Hi Anastasia,
>
> On Mon, 2010-06-21 at 19:55 +0200, Anastasia Gioti wrote:
>> hello,
>> I was wondering whether it is possible to give MAUVE a file different
>> from a genbank file in case one wants to load annotations on the
>> aligned genomes. I find this particularly useful when looking at my
>> synteny blocks, but I don't have genbank files for most of my
>> genomes.
>> I have gff files from annotations made with MAKER, but I don't see
>> that option in the manual. Maybe in the command line version?
>> I also tried to create genbank -type files ( i don't want to submit
>> yet) but although these loaded successfully, I only see the name of
>> the scaffold, not related features. My way of creating genbank-type
>> files may be too rough (i don't know how to really do it, used
>> DNAnnotator and merged output files) but it does create a features+
>> sequence file (though features are all annotated as exons). Any help
>> would be appreciated!
>
> Currently the Mauve GUI only fully supports GenBank for sequence
> annotation viewing. However, the GUI only shows the following feature
> types by default: CDS, tRNA, rRNA, misc_RNA, and repeat_region.
> Notice
> that exon is not in that list. So if you change all exon
> annotations to
> CDS, for example, they should appear in the GUI.
> As for other formats, there is partial support for INSDseq XML format,
> and using it requires editing the XMFA file to indicate that the
> AnnotationFormat is INSDseq. The command-line aligner can not parse
> the
> XML, but the GUI can display the above-listed feature types from XML.
>
> At some point it would be great if the GUI was more configurable and
> flexible with annotation viewing, it's something us Mauve developers
> have been planning for a while but haven't been able to push out in a
> release yet for various reasons.
>
> Hope that helps,
> -Aaron
>
>
Anastasia Gioti
Post-Doc, Evolutionary Biology Department
Upssala University
Norbyvägen 18D
SE-752 36 UPPSALA
[email protected]
Tel: +46-18-471 2837
Fax: +46-18-471 6310
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