how to create blast functionality on GBrowse

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how to create blast functionality on GBrowse

Tyagi, Eishita
Hi,

Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.

Thanks
Eishita

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Re: how to create blast functionality on GBrowse

J.M.P. Alves
Hi,

The way I have implemented here with the plugin I know, the BLAST is
actually of your sequence (from GBrowse) against NCBI databases and run
on NCBI servers. Let me know if that's what you're after and I'll give
more details on how to do it.

If you want to see it in action, visit one of our GBrowse instances here:
http://www.gardnerella.mic.vcu.edu

Use the rubber-band selection on the detail area (the coordinates part)
and a pop-up menu will show. Select "submit selection to NCBI BLAST" and
a new page will open where you can choose parameters and finally submit.

Cheers
J

Tyagi, Eishita wrote:

> Hi,
>
> Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.
>
> Thanks
> Eishita
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: how to create blast functionality on GBrowse

Shane Brubaker
We have used GBlast, a cgi-bin script.  I think someone on this list actually wrote it.


-----Original Message-----
From: J.M.P. Alves [mailto:[hidden email]]
Sent: Tuesday, June 22, 2010 1:40 PM
To: Tyagi, Eishita
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] how to create blast functionality on GBrowse

Hi,

The way I have implemented here with the plugin I know, the BLAST is
actually of your sequence (from GBrowse) against NCBI databases and run
on NCBI servers. Let me know if that's what you're after and I'll give
more details on how to do it.

If you want to see it in action, visit one of our GBrowse instances here:
http://www.gardnerella.mic.vcu.edu

Use the rubber-band selection on the detail area (the coordinates part)
and a pop-up menu will show. Select "submit selection to NCBI BLAST" and
a new page will open where you can choose parameters and finally submit.

Cheers
J

Tyagi, Eishita wrote:

> Hi,
>
> Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.
>
> Thanks
> Eishita
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: how to create blast functionality on GBrowse

Adam Witney
In reply to this post by J.M.P. Alves

Hi,

this is a change of subject, but I am intrigued by how you have your backend setup as your browser seems very responsive! Do you use mysql/postgresql? Any particular optimisations you have?

thanks

adam


On 22 Jun 2010, at 21:40, J.M.P. Alves wrote:

> Hi,
>
> The way I have implemented here with the plugin I know, the BLAST is
> actually of your sequence (from GBrowse) against NCBI databases and run
> on NCBI servers. Let me know if that's what you're after and I'll give
> more details on how to do it.
>
> If you want to see it in action, visit one of our GBrowse instances here:
> http://www.gardnerella.mic.vcu.edu
>
> Use the rubber-band selection on the detail area (the coordinates part)
> and a pop-up menu will show. Select "submit selection to NCBI BLAST" and
> a new page will open where you can choose parameters and finally submit.
>
> Cheers
> J
>
> Tyagi, Eishita wrote:
>> Hi,
>>
>> Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.
>>
>> Thanks
>> Eishita
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: how to create blast functionality on GBrowse

J.M.P. Alves
Hi, Adam.

Nothing too fancy, it's a 5 year old Dell desktop running it. That is
GBrowse2 running using FastCGI and mod_perl, as described in the How
To's first two topics:

http://gmod.org/wiki/GBrowse_2.0_HOWTO#Advanced_Installation_Topics

After testing the two of them separately as described in the tutorials,
I changed my gbrowse2.conf (the one living at /etc/apache2/conf.d/) to:

Alias        "/gbrowse2/i/" "/var/tmp/gbrowse2/images/"
Alias        "/gbrowse2"    "/var/www/gbrowse2"
ScriptAlias  "/gb2"      "/usr/lib/cgi-bin/gb2"

<Directory "/var/www/gbrowse2">
   AllowOverride Options
   Options -Indexes -MultiViews +FollowSymLinks
   Order allow,deny
   Allow from all
</Directory>

<Directory "/var/tmp/gbrowse2/images/">
   Order allow,deny
   Allow from all
</Directory>

<Directory "/usr/lib/cgi-bin/gb2">

   SetEnv GBROWSE_CONF   "/etc/gbrowse2"
   SetHandler   fastcgi-script
   PerlResponseHandler ModPerl::Registry
   PerlOptions +ParseHeaders
</Directory>

   FastCgiConfig  -initial-env GBROWSE_CONF=/etc/gbrowse2


So far, it's worked fine, and it makes a very big difference in how
responsive the browser is. In my quick tests, it appears that what makes
more of a difference is the FastCGI modification, if you decide to keep
just one of them (the right prerequisite packages have to be installed,
as described in the docs).

Regards
J

Adam Witney wrote:

> Hi,
>
> this is a change of subject, but I am intrigued by how you have your backend setup as your browser seems very responsive! Do you use mysql/postgresql? Any particular optimisations you have?
>
> thanks
>
> adam
>
>
> On 22 Jun 2010, at 21:40, J.M.P. Alves wrote:
>
>> Hi,
>>
>> The way I have implemented here with the plugin I know, the BLAST is
>> actually of your sequence (from GBrowse) against NCBI databases and run
>> on NCBI servers. Let me know if that's what you're after and I'll give
>> more details on how to do it.
>>
>> If you want to see it in action, visit one of our GBrowse instances here:
>> http://www.gardnerella.mic.vcu.edu
>>
>> Use the rubber-band selection on the detail area (the coordinates part)
>> and a pop-up menu will show. Select "submit selection to NCBI BLAST" and
>> a new page will open where you can choose parameters and finally submit.
>>
>> Cheers
>> J
>>
>> Tyagi, Eishita wrote:
>>> Hi,
>>>
>>> Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.
>>>
>>> Thanks
>>> Eishita
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: how to create blast functionality on GBrowse

J.M.P. Alves
In reply to this post by Tyagi, Eishita
Hi,

Sorry for the delay in answering. To enable the BLAST against NCBI
functionality, I have the following in my conf files.

In GBrowse.conf, the plugin line looks like:
plugins  = FastaDumper RestrictionAnnotator AttributeHiliter Submitter
SequenceDumper

(all in one line, if email software broke it in parts)

And in the data source's specific conf file, have to add something like:

[Submitter:plugin]
submitter = [NCBI_BLAST]
             confirm   = 1
             url       = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
             seq_label = QUERY
             PAGE      = Nucleotides
             extra_html = BLAST type:
                          <SELECT name="PROGRAM">
                            <OPTION VALUE="blastn">blastn</OPTION>
                            <OPTION VALUE="blastx">blastx</OPTION>
                            <OPTION VALUE="tblastx">tblastx</OPTION>
                          </SELECT><BR>
                          Database:
                          <SELECT name="DATABASE">
                            <OPTION VALUE="nr">nr/nt</OPTION>
                            <OPTION VALUE="est">est</OPTION>
                            <OPTION VALUE="refseq_rna">refseq_rna</OPTION>
                            <OPTION
VALUE="refseq_genomic">refseq_genomic</OPTION>
                            <OPTION VALUE="env_nt">env_nt</OPTION>
                            <OPTION VALUE="chromosome">chromosome</OPTION>
                          </SELECT><br>
                          E-value threshold: <input name="EXPECT"
size="10" type="text" value="1e-6"><br>
                          Filter low complexity regions <input
type="checkbox" name="FILTER" value="L" checked><br>
                          Mask for lookup table only <input
type="checkbox" name="FILTER" value="m" checked><br>
                          Mask lower case letters <input type="checkbox"
name="LCASE_MASK"><br>
             CLIENT    = web
             CMD       = put

I also have the following, which is needed for the FASTA retrieval, but
might also be needed for the BLAST submitter (I'm not sure). Try without
it first and if it does not work, try adding this.

[TOOLTIPS]
full_sequence = sub {
                   my $args = shift;
                   my $feat = $args->{feature};
                   my $name  = $feat->display_name;
                   my $seq = $feat->seq->seq;
                   $seq =~ s/(\S{75})/$1\n/g;
                   return "<pre>>$name\n$seq</pre>";
                }


Defaults can be changed in these lines (e.g. which programs you want to
call, databases to include, E-value, etc.). If you are running GBrowse
1.x, both the plugin line and this second part go in the same file (the
data source .conf file). I hope that works for you.

Cheers
J

Tyagi, Eishita wrote:

> Also, could you please send me more details on how you did the blast against the NCBI database too.
>
>
>
> ----- Original Message -----
> From: "Eishita Tyagi" <[hidden email]>
> To: "J.M.P. Alves" <[hidden email]>
> Sent: Wednesday, June 23, 2010 7:48:56 AM GMT -05:00 US/Canada Eastern
> Subject: Re: [Gmod-gbrowse] how to create blast functionality on GBrowse
>
> Hi,
>
> Actually what I wanted was an input of aay sequence from a user or a fasta file input and that input would be blasted against the sequences loaded in the gbrowse.
> Please let me know if you could help me with that.
>
> Thanks
> Eishita
>
>
>  
> ----- Original Message -----
> From: "J.M.P. Alves" <[hidden email]>
> To: "Eishita Tyagi" <[hidden email]>
> Cc: [hidden email]
> Sent: Tuesday, June 22, 2010 4:40:20 PM GMT -05:00 US/Canada Eastern
> Subject: Re: [Gmod-gbrowse] how to create blast functionality on GBrowse
>
> Hi,
>
> The way I have implemented here with the plugin I know, the BLAST is
> actually of your sequence (from GBrowse) against NCBI databases and run
> on NCBI servers. Let me know if that's what you're after and I'll give
> more details on how to do it.
>
> If you want to see it in action, visit one of our GBrowse instances here:
> http://www.gardnerella.mic.vcu.edu
>
> Use the rubber-band selection on the detail area (the coordinates part)
> and a pop-up menu will show. Select "submit selection to NCBI BLAST" and
> a new page will open where you can choose parameters and finally submit.
>
> Cheers
> J
>
> Tyagi, Eishita wrote:
>> Hi,
>>
>> Could anyone please guide me as to how I could create a blast functionality on my genome browser. I saw some plugins that referred to it but, it wasn't very clear to me. Also could you please tell me how to use these plugins in my browser. I am very new to gbrowse so I would really appreciate the  help.
>>
>> Thanks
>> Eishita
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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