Blast server

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Blast server

mictadlo
Hi,
I found this BLAST server  (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

--
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Reply | Threaded
Open this post in threaded view
|

Re: Blast server

nathandunn

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/ 


This should work for either blat or blast  (https://blast.ncbi.nlm.nih.gov/Blast.cgi ) . 

This is provided by default with Docker. 




2 - The i5k workspace is here: https://github.com/NAL-i5K

3 - https://github.com/GMOD/jblast-jbconnect-hook ?  (For JBrowse) maintained by Eric Yao.

4 - I believe the galaxy.eu server has one:  https://annotation.usegalaxy.eu/

5 - 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 <[hidden email]> wrote:

Hi,
I found this BLAST server  (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

--
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].