I have just started using B2G, and I found this tool is a quite useful
for studying on non-model organisms. Now I am working with around 20k
sequences. What I would ask all of you are;
1. I am triying to import a relatively large xml file of BLAST result
(BLASTX, v2.2.10) of ~20k query sequences, but it seems to take a
quite long time, maybe more than a day. I wonder if this is normal or
not. B2G (v.2.1.1, 2048M version) is running on MacOS 10.4/J2SE5.0,
PowerPC G5 Quad 2.5GHz/8GB RAM.
2. From the 'Blast/IPS Result' window, an web browser program may be
launched when sequence link is clicked. But in my case, a window of
'Coose the browser ro use' showed up and even if I selected browsers
(Safari, FireFox), it never worked. In the 'Application Messages'
window, an error message 'Error with choosen Browser! /Applications/
Firefox.app: cannot execute' was indicated. Can I solve this problem
by any means or is this a bug especially on MacOS platform?
Dear Hiro, we are aware of the performance problem with large xml files and do have that on our todo list. Meanwhile I would recommend to test first the import of a small file and to try further mapping and annotation functions to see if everything works fine. If everything turn out as wished import overnight the big set. But yes, in the moment it takes a while especially if you have many hits per sequence.
Normally the "choose browser" function should worked fine. If you wish to reset the configuration to try another executable of a different browser find the blast2go.properties file and reset the browser settings. I have no Mac close right now to test but on my Fedora things work fine with Firefox.
Best regards, Stefan Goetz
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-------------------------------------------- Stefan Götz Bioinformatics Department Centro de Investigación Príncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgo...@cipf.es http://bioinfo.cipf.es --------------------------------------------
> I have just started using B2G, and I found this tool is a quite useful > for studying on non-model organisms. Now I am working with around 20k > sequences. What I would ask all of you are;
> 1. I am triying to import a relatively large xml file of BLAST result > (BLASTX, v2.2.10) of ~20k query sequences, but it seems to take a > quite long time, maybe more than a day. I wonder if this is normal or > not. B2G (v.2.1.1, 2048M version) is running on MacOS 10.4/J2SE5.0, > PowerPC G5 Quad 2.5GHz/8GB RAM.
> 2. From the 'Blast/IPS Result' window, an web browser program may be > launched when sequence link is clicked. But in my case, a window of > 'Coose the browser ro use' showed up and even if I selected browsers > (Safari, FireFox), it never worked. In the 'Application Messages' > window, an error message 'Error with choosen Browser! /Applications/ > Firefox.app: cannot execute' was indicated. Can I solve this problem > by any means or is this a bug especially on MacOS platform?
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