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?

Thank you in advance,

Michal

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

[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/ 

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 ) . 

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].