Re: [Gmod-ajax] [apollo] Blast server

[Nathan D. <nat...@lb...>]

Oh, even easier in just using the `Save sequence` drop down.  Not sure why I forgot that. 



Nathan


> On Mar 11, 2021, at 4:25 PM, Nathan Dunn <nat...@lb...> wrote:
> 
> 
> For the reference sequence track at the top you choose:
> 
> <PastedGraphic-1.tiff>
> 
> And then the highlighted region:
> 
> <PastedGraphic-2.tiff>
> 
> 
> With respect to JB-connect, I don’t think we’d tried that experiment, but I don’t know of any reason it wouldn’t work, though it may require a bit of configuration.  
> 
> Nathan
> 
> 
> 
>> On Mar 11, 2021, at 4:01 PM, Michał T. Lorenc <m.t...@gm... <mailto:m.t...@gm...>> wrote:
>> 
>> Hi Nathan,
>> Thank you for the list. It appears that NAL-i5k uses under the hood https://github.com/NAL-i5K/django-blast <https://github.com/NAL-i5K/django-blast> . By any chance, do you know how to allow the user to click on the blast result, and apollo will open and highlight the BLAST hit region?
>> 
>> I am also interested in Eric's https://github.com/GMOD/jblast-jbconnect-hook <https://github.com/GMOD/jblast-jbconnect-hook> . Is the installation documentation (https://jblast.readthedocs.io/en/latest/#install <https://jblast.readthedocs.io/en/latest/#install>) compatible with Apollo?
>> 
>> Thank you in advance,
>> 
>> Michal
>> 
>> On Fri, Dec 11, 2020 at 10:12 AM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
>> 
>> There are a few options (at least for Apollo):
>> 
>> 
>> 1 - if you configure BLAT binaries, you can just use those directly: https://hgdownload.soe.ucsc.edu/admin/exe/ <https://hgdownload.soe.ucsc.edu/admin/exe/> 
>> 
>> https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blast#search-tools <https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blast#search-tools>
>> 
>> This should work for either blat or blast  (https://blast.ncbi.nlm.nih.gov/Blast.cgi <https://blast.ncbi.nlm.nih.gov/Blast.cgi> ) . 
>> 
>> This is provided by default with Docker. 
>> 
>> <PastedGraphic-3.tiff>
>> 
>> 
>> 
>> 2 - The i5k workspace is here: https://github.com/NAL-i5K <https://github.com/NAL-i5K>
>> 
>> 3 - https://github.com/GMOD/jblast-jbconnect-hook <https://github.com/GMOD/jblast-jbconnect-hook> ?  (For JBrowse) maintained by Eric Yao.
>> 
>> 4 - I believe the galaxy.eu <http://galaxy.eu/> server has one:  https://annotation.usegalaxy.eu/ <https://annotation.usegalaxy.eu/>
>> 
>> 5 - https://i5k.nal.usda.gov/webapp/blast/ <https://i5k.nal.usda.gov/webapp/blast/>  (this is probably pretty specialized)
>> 
>> I’m sure there are other ones. 
>> 
>> 
>> Nathan
>> 
>> 
>>> On Dec 10, 2020, at 3:57 PM, Michał T. Lorenc <m.t...@gm... <mailto:m.t...@gm...>> wrote:
>>> 
>>> Hi,
>>> I found this BLAST server  (https://solgenomics.net/tools/blast/ <https://solgenomics.net/tools/blast/>) which is able to highlight matching protein sequence. Unfortunately, this one is not open source and not available for download. By any change, do any one know a Blast server which can be downloaded, highlight maching protein sequence and allows to jump to Jbrowse/Apollo?
>>> 
>>> 
>>> <image.png>
>>> 
>>> 
>>> <image.png>
>>> 
>>> <image.png>
>>> Thank you in advance,
>>> 
>>> Michal
>> 
>> 
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