Sequence not appear on gbrowse_details

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Sequence not appear on gbrowse_details

Irwandwiyanto
I tried running gbrowse2 accordance with the installation instructions , gbrowse2 already working on localhost and graph databases have also appeared , but when trying to view details gene DNA sequence does not appear , is there any thing wrong in the installation ??
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Re: Sequence not appear on gbrowse_details

Alexey Morozov
You mean DNA sequence as in ACTGTACA... thingie? Gbrowse doesn't display it directly: you should either view object properties (default function for click, as I recall) or use sequence download addons,

2015-01-28 12:41 GMT+08:00 Irwandwiyanto <[hidden email]>:
I tried running gbrowse2 accordance with the installation instructions ,
gbrowse2 already working on localhost and graph databases have also appeared
, but when trying to view details gene DNA sequence does not appear , is
there any thing wrong in the installation ??



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Re: Sequence not appear on gbrowse_details

Irwandwiyanto
I tried to create a new data but still does not appear on gbrowse_detailsexample
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Re: Sequence not appear on gbrowse_details

Alexey Morozov
I'm not sure I get the question. The sequence shows okay for yeast, but your genome DB doesn't open correctly? Or is there something wrong with how gbrowse_details displays yeast sequence?
If it's your genome, please send Gbrowse.conf and your DB's conf file.

2015-01-28 15:39 GMT+08:00 Irwandwiyanto <[hidden email]>:
I tried to create a new data but still does not appear on gbrowse_details
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5713056/sad.jpg>



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Re: Sequence not appear on gbrowse_details

Irwandwiyanto
this is link GBrowse.conf and databases
http://goo.gl/QRZZTd
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Re: Sequence not appear on gbrowse_details

Alexey Morozov
That's weird; configs seem alright to me. What file format do you store your sequences in? If it's GFF3, don't forget to include separate definition lines for scaffolds or contigs. Example:

scaffold00001 newbler contig 1 1348726 . . . ID=scaffold00001;Name=scaffold00001
.....other stuff....
scaffold00001 maker gene 56082 56739 . + . ID=4447-gene;Name=4447-gene
scaffold00001 maker mRNA 56082 56739 . + . ID=4447;Parent=4447-gene;Name=4447;_AED=0.02;_eAED=0.02;_QI=0|0|0|1|1|1|2|0|184
scaffold00001 maker exon 56082 56220 . + . ID=4447:exon:0;Parent=4447
scaffold00001 maker exon 56324 56739 . + . ID=4447:exon:1;Parent=4447
scaffold00001 maker CDS 56082 56220 . + 0 ID=4447:cds;Parent=4447
scaffold00001 maker CDS 56324 56739 . + 2 ID=4447:cds;Parent=4447
scaffold00001 maker gene 63275 63728 . + . ID=4448-gene;Name=4448-gene
scaffold00001 maker mRNA 63275 63728 . + . ID=4448;Parent=4448-gene;Name=4448;_AED=0.02;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|97;Note=mitochondrial import inner membrane translocase subunit tim9-like;Ontology_term=GO:0016020,GO:0046872,GO:0005739,GO:0015031
.......other stuff......
>scaffold00001
ACGTACAAACTGAAG....

The first line is the key. If you don't include it, the fasta sequences in the end (or in the separate file) don't get parsed.

2015-01-28 16:22 GMT+08:00 Irwandwiyanto <[hidden email]>:
this is link GBrowse.conf and databases
http://goo.gl/QRZZTd



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Re: Sequence not appear on gbrowse_details

Irwandwiyanto
this my databases
##gff-version 3
##sequence-region chrLG2 1 66492657

chrLG2 GlimmerHMM contig 1 66492657 . + . ID=chrLG2;Name=chrLG2
chrLG2 GlimmerHMM mRNA 47748452 47748949 . + . ID=p5_sc00005.V1.gene1000;Name=Os02g0307900
chrLG2 GlimmerHMM CDS 47748452 47748949 . + . ID=p5_sc00005.cds1000.1;Parent=p5_sc00005.V1.gene1000;Name=Os02g0307900;Note=single-exon
chrLG2 GlimmerHMM mRNA 42116662 42123008 . + . ID=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088
chrLG2 GlimmerHMM CDS 42116662 42118543 . + . ID=p5_sc00005.cds100.1;Parent=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088;Note=initial-exon
 
>chrLG2
CCCTAAAcCCTAAACCCTAAACCCTAAACACGAAATCCAAAATCCTAACCCCAAAGTCCTAAACCCTAAG
CCTTAAATTATATACCCTAAATTCaAAATCATAAGCCCTAAACCCTAAGCCCTAAAcCCTAAATCTTAAA

I try to follow what you suggest but the result is still the same
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Re: Sequence not appear on gbrowse_details

Irwandwiyanto
Dear Mr  Alexey Morozov
i try installing gbrowse again with ubuntu 15.04, after installing any error

Forbidden

You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this server.
Apache/2.4.7 (Ubuntu) Server at 10.88.25.48 Port 80

do you help me?

best regards
Duwi Irwanto

2015-01-28 16:38 GMT+07:00 Irwandwiyanto [via Generic Model Organism System Database] <[hidden email]>:
this my databases
##gff-version 3
##sequence-region chrLG2 1 66492657

chrLG2 GlimmerHMM contig 1 66492657 . + . ID=chrLG2;Name=chrLG2
chrLG2 GlimmerHMM mRNA 47748452 47748949 . + . ID=p5_sc00005.V1.gene1000;Name=Os02g0307900
chrLG2 GlimmerHMM CDS 47748452 47748949 . + . ID=p5_sc00005.cds1000.1;Parent=p5_sc00005.V1.gene1000;Name=Os02g0307900;Note=single-exon
chrLG2 GlimmerHMM mRNA 42116662 42123008 . + . ID=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088
chrLG2 GlimmerHMM CDS 42116662 42118543 . + . ID=p5_sc00005.cds100.1;Parent=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088;Note=initial-exon
 
>chrLG2
CCCTAAAcCCTAAACCCTAAACCCTAAACACGAAATCCAAAATCCTAACCCCAAAGTCCTAAACCCTAAG
CCTTAAATTATATACCCTAAATTCaAAATCATAAGCCCTAAACCCTAAGCCCTAAAcCCTAAATCTTAAA

I try to follow what you suggest but the result is still the same



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