Hi Anastasia,
GenBank file format issues are tricky. I think the problem is in your
coordinates (aka the Location descriptors), although it might be a weirdness
introduced by email. Your file has the format
> CDS
>join
>(348
>..
>606,560
>..
>606,674
>..
>749,674
>..
>749,823
>..1370,823..1370,1423..1454,1423..1454,1527..1726,1527..1812,1881..2319)
While it should all be on a single line:
CDS
join(348..606,560..606,674..749,674..749,823..1370,823..1370,1423..1454,1423..1454,1527..1726,1527..1812,1881..2319)
(will probably get wrapped by email)
But even after reformatting, your join statement may not be valid:
The first two intervals overlap (348..606 and 560..606) -- I am not sure this
is allowed; smaller overlaps, e.g. those due to -1 or -2 ribosomal frameshifts,
are valid but often raise errors with some parsers (not sure about Mauve)
A number of intervals are repeated: 674..749, 823..1370, and 1423..1454; Mauve
may not be able tp parse that?
Try simpler join statements to see if they work OK.
- Guy
Dr. Guy Plunkett III
Laboratory of Genetics voice: (608) 890-0189
University of Wisconsin fax: (608) 262-2976
425G Henry Mall Rm 5428 email: [email protected]
Madison, WI 53706-1580 web:
http://www.genome.wisc.edu/information/gplunkett.html
On 7/2/10, Anastasia Gioti wrote:
>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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