Setting up Swissport DAS with GBrowse

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Setting up Swissport DAS with GBrowse

Ioannis Kirmitzoglou
Hi all,

I have configured and modified a Gbrowse instance to work with protein data. I've loaded the latest version of swissprot. Here's the link to the browser


The way I've set it up every protein sequence appears as a different "chromosome" in the browser. All entries are stored in a mysql database.

I would like to also include some external tracks from the Swissprot Das server. 
Here's a link to the DAS server that matches the default protein shown in my Gbrowse
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=002L_FRG3G

Following the instructions here http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod I used make_das_conf.pl to generate a config file for GBrowse. Here's the link for that source http://repeat.biol.ucy.ac.cy/mgb2/gbrowse/uniprot_das/.
As you will notice, it doesn't work :(

Am also pasting part of the config file that was generated and used

[GENERAL]
description   = UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
db_adaptor    = Bio::Das
db_args       = -source http://www.ebi.ac.uk/das-srv/uniprot/das
       -dsn    uniprot
                

# examples to show in the introduction
examples = A0A000 A0A001 A0A002 A0A003 A0A004 A0A005 A0A006 A0A007 A0A008 A0A009 A0A010 A0A011 A0A012 A0A013 A0A014 A0A015 A0A016 A0A017 A0A018 A0A019 A0A020 A0A021 A0A022 A0A023 A0A024 A0A025 A0A026 A0A027 A0A028 A0A029 A0A030 A0A031 A0A032 A0A033 A0A034 A0A035 A0A036 A0A037 A0A038 A0A039 A0A040 A0A041 A0A042 A0A043 A0A044 A0A045 A0A046 A0A047 A0A048 A0A049 A0A050 A0A051 A0A052 A0A053 A0A054 A0A055 A0A056 A0A057 A0A058 A0A059 A0A060 A0A061 A0A062 A0A063 A0A064 A0A066 A0A067 A0A073 A0A074 A0A075 A0A076 A0A077 A0A078 A0A079 A0A080 A0A081 A0A082 A0A083 A0A084 A0A085 A0A086 A0A087 A0A088 A0A089 A0A090 A0A091 A0A092 A0A093 A0A097 A0A098 A0A099 A0A0A0 A0A0A1 A0A0A2 A0A0A3 A0A0A4 A0A0A5 A0A0A6 A0A0A7 A0A0B1


aggregators = BS{BS}
       SO{SO}
       MOD{MOD}

########################
# Default glyph settings
########################

[TRACK DEFAULTS]
glyph         = segments
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
label         = 1
description   = 1

[BS_01006]
feature      = BS:01006
bgcolor      = cyan
das category = Comment
key          = BS:01006
citation     = These are BS:01006 features.

[BS_01025]
feature      = BS:01025
bgcolor      = blue
das category = Comment
key          = BS:01025
citation     = These are BS:01025 features.

[SO_0001067]
feature      = SO:0001067
bgcolor      = red
das category = Region
key          = SO:0001067
citation     = These are SO:0001067 features.

[SO_0001149]
feature      = SO:0001149
bgcolor      = yellow
das category = Sequence variation
key          = SO:0001149
citation     = These are SO:0001149 features.


This is the first time I'm trying to setup DAS with Gbrowse and I must admit it proved much more challenging than I originally thought.

Any help would be much apreciated.

King regards, 
Ioannis


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Re: Setting up Swissport DAS with GBrowse

Scott Cain
Hi Ioannis,

There are a few things you can try to debug:

1. Try adding the track as a custom track through the user interface (via add URL under custom tracks),

2. Try turning the yeast sample data back on, and try adding as a custom track this from UCSC:


It might be a bit slow, but it should work.  If it doesn't, perhaps there is something wrong with Bio::Das.  If the das from UCSC does work, then you may have a bit of a problem: my recollection is that there are a few "flavors" of das1, and it may be that the das1 that SwissProt serves is not the das1 that GBrowse speaks.

Scott



On Fri, Apr 25, 2014 at 2:17 PM, Ioannis Kirmitzoglou <[hidden email]> wrote:
Hi all,

I have configured and modified a Gbrowse instance to work with protein data. I've loaded the latest version of swissprot. Here's the link to the browser


The way I've set it up every protein sequence appears as a different "chromosome" in the browser. All entries are stored in a mysql database.

I would like to also include some external tracks from the Swissprot Das server. 
Here's a link to the DAS server that matches the default protein shown in my Gbrowse
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=002L_FRG3G

Following the instructions here http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod I used make_das_conf.pl to generate a config file for GBrowse. Here's the link for that source http://repeat.biol.ucy.ac.cy/mgb2/gbrowse/uniprot_das/.
As you will notice, it doesn't work :(

Am also pasting part of the config file that was generated and used

[GENERAL]
description   = UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
db_adaptor    = Bio::Das
db_args       = -source http://www.ebi.ac.uk/das-srv/uniprot/das
       -dsn    uniprot
                

# examples to show in the introduction
examples = A0A000 A0A001 A0A002 A0A003 A0A004 A0A005 A0A006 A0A007 A0A008 A0A009 A0A010 A0A011 A0A012 A0A013 A0A014 A0A015 A0A016 A0A017 A0A018 A0A019 A0A020 A0A021 A0A022 A0A023 A0A024 A0A025 A0A026 A0A027 A0A028 A0A029 A0A030 A0A031 A0A032 A0A033 A0A034 A0A035 A0A036 A0A037 A0A038 A0A039 A0A040 A0A041 A0A042 A0A043 A0A044 A0A045 A0A046 A0A047 A0A048 A0A049 A0A050 A0A051 A0A052 A0A053 A0A054 A0A055 A0A056 A0A057 A0A058 A0A059 A0A060 A0A061 A0A062 A0A063 A0A064 A0A066 A0A067 A0A073 A0A074 A0A075 A0A076 A0A077 A0A078 A0A079 A0A080 A0A081 A0A082 A0A083 A0A084 A0A085 A0A086 A0A087 A0A088 A0A089 A0A090 A0A091 A0A092 A0A093 A0A097 A0A098 A0A099 A0A0A0 A0A0A1 A0A0A2 A0A0A3 A0A0A4 A0A0A5 A0A0A6 A0A0A7 A0A0B1


aggregators = BS{BS}
       SO{SO}
       MOD{MOD}

########################
# Default glyph settings
########################

[TRACK DEFAULTS]
glyph         = segments
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
label         = 1
description   = 1

[BS_01006]
feature      = BS:01006
bgcolor      = cyan
das category = Comment
key          = BS:01006
citation     = These are BS:01006 features.

[BS_01025]
feature      = BS:01025
bgcolor      = blue
das category = Comment
key          = BS:01025
citation     = These are BS:01025 features.

[SO_0001067]
feature      = SO:0001067
bgcolor      = red
das category = Region
key          = SO:0001067
citation     = These are SO:0001067 features.

[SO_0001149]
feature      = SO:0001149
bgcolor      = yellow
das category = Sequence variation
key          = SO:0001149
citation     = These are SO:0001149 features.


This is the first time I'm trying to setup DAS with Gbrowse and I must admit it proved much more challenging than I originally thought.

Any help would be much apreciated.

King regards, 
Ioannis


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Setting up Swissport DAS with GBrowse

Ioannis Kirmitzoglou

Hi Scott,

 

Thanks for your help.

 

1.      Try adding the track as a custom track through the user interface (via add URL under custom tracks),

 

Doesn’t work :(

 

2. Try turning the yeast sample data back on, and try adding as a custom track this from UCSC:

 

 

It might be a bit slow, but it should work.  If it doesn't, perhaps there is something wrong with Bio::Das.  If the das from UCSC does work, then you may have a bit of a problem: my recollection is that there are a few "flavors" of das1, and it may be that the das1 that SwissProt serves is not the das1 that GBrowse speaks.

 

When adding the link through the custom tracks panel is not working. Using the make_das_conf.pl to make a new database in Gbrowse works fine!!

 

Does this means that uniprot das is not compatible with Gbrowse? Any suggestions on how to overcome this (e.g. is there a DAS server that can act as a proxy and convert uniprot das xmls to something GBrowse can consume?)

 

Many thanks Again,

 

Ioannis

 

On Fri, Apr 25, 2014 at 2:17 PM, Ioannis Kirmitzoglou <[hidden email]> wrote:

Hi all,

 

I have configured and modified a Gbrowse instance to work with protein data. I've loaded the latest version of swissprot. Here's the link to the browser

 

 

The way I've set it up every protein sequence appears as a different "chromosome" in the browser. All entries are stored in a mysql database.

 

I would like to also include some external tracks from the Swissprot Das server. 
Here's a link to the DAS server that matches the default protein shown in my Gbrowse
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=002L_FRG3G

 

Following the instructions here http://search.cpan.org/dist/GBrowse/docs/pod/DAS_HOWTO.pod I used make_das_conf.pl to generate a config file for GBrowse. Here's the link for that source http://repeat.biol.ucy.ac.cy/mgb2/gbrowse/uniprot_das/.

As you will notice, it doesn't work :(

 

Am also pasting part of the config file that was generated and used

 

[GENERAL]

description   = UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

db_adaptor    = Bio::Das

db_args       = -source http://www.ebi.ac.uk/das-srv/uniprot/das

       -dsn    uniprot

                

 

# examples to show in the introduction

examples = A0A000 A0A001 A0A002 A0A003 A0A004 A0A005 A0A006 A0A007 A0A008 A0A009 A0A010 A0A011 A0A012 A0A013 A0A014 A0A015 A0A016 A0A017 A0A018 A0A019 A0A020 A0A021 A0A022 A0A023 A0A024 A0A025 A0A026 A0A027 A0A028 A0A029 A0A030 A0A031 A0A032 A0A033 A0A034 A0A035 A0A036 A0A037 A0A038 A0A039 A0A040 A0A041 A0A042 A0A043 A0A044 A0A045 A0A046 A0A047 A0A048 A0A049 A0A050 A0A051 A0A052 A0A053 A0A054 A0A055 A0A056 A0A057 A0A058 A0A059 A0A060 A0A061 A0A062 A0A063 A0A064 A0A066 A0A067 A0A073 A0A074 A0A075 A0A076 A0A077 A0A078 A0A079 A0A080 A0A081 A0A082 A0A083 A0A084 A0A085 A0A086 A0A087 A0A088 A0A089 A0A090 A0A091 A0A092 A0A093 A0A097 A0A098 A0A099 A0A0A0 A0A0A1 A0A0A2 A0A0A3 A0A0A4 A0A0A5 A0A0A6 A0A0A7 A0A0B1

 

 

aggregators = BS{BS}

       SO{SO}

       MOD{MOD}

 

########################

# Default glyph settings

########################

 

[TRACK DEFAULTS]

glyph         = segments

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100

label         = 1

description   = 1

 

[BS_01006]

feature      = BS:01006

bgcolor      = cyan

das category = Comment

key          = BS:01006

citation     = These are BS:01006 features.

 

[BS_01025]

feature      = BS:01025

bgcolor      = blue

das category = Comment

key          = BS:01025

citation     = These are BS:01025 features.

 

[SO_0001067]

feature      = SO:0001067

bgcolor      = red

das category = Region

key          = SO:0001067

citation     = These are SO:0001067 features.

 

[SO_0001149]

feature      = SO:0001149

bgcolor      = yellow

das category = Sequence variation

key          = SO:0001149

citation     = These are SO:0001149 features.

 

 

This is the first time I'm trying to setup DAS with Gbrowse and I must admit it proved much more challenging than I originally thought.

 

Any help would be much apreciated.

 

King regards, 

Ioannis


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Get Started Now And Turn Your Intranet Into A Collaboration Platform
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