WebFlaGs

We have a new feature of webFlaGs.se! Now possible to submit a single sequence or accession. Homologues are automatically found with BLASTP against the RefSeq db and used as FlaGs input. Previous users might have to refresh to clear the cache & see the new input page

We had an issue with webFlaGs and uORF4u jobs getting stuck in the input validation step, but should be working fine now

We are looking for a new PhD student to join us on our adventures in computational sequence and structural analyses of bacteriophage proteins atkinson-lab.com/phd-position-a… You will be part of the new and exciting @scilifelab DDLS research school

Please use this link to access webflags at the moment server.atkinson-lab.com/webflags Something up with the forwarding for the .se domain

Hurray, we’ve fixed it! Webflags.se is taking submissions again!

The problem seems to be that we can't access @ncbi ftp.ncbi.nih.gov from Lund University servers

local FlaGs2 seems unaffected

We're aware of some issue this weekend causing FlaGs to fail. Looking into it...

An interactive visualization of conserved gene neighborhoods now on corewiki.uni-goettingen.de (#SubtiWiki's next version)! It features clusters created with @webflags1 . Big thanks to Tom Nowak for his work and @gem__atkinson for the great FlaGs tool! @IMPRS_GS #bacillus #MOTY

Looks like the @NCBI protein database is a bit wobbly this morning. webFlaGs might be slow and/or submissions might fail.

Hello! LU-Fold now has an X presence! We are a Lund University facility for high throughput protein complex structure prediction. Follow for updates and click here for more info and request support atkinson-lab.com/lu-fold/

That’s great to hear, thank you for the update!

We're having more slow and failed jobs than usual today due to getting a lot of the dreaded Bad Gateway errors for @NCBI searches. Hoping it's 'just one of those days'...

Just a heads up that there's currently an @NCBI bug affecting FlaGs: some valid RefSeq accessions are not associated with their corresponding assembly IDs in the Identical Protein Group (IPG) data. I'm in contact with the lovely people at NCBI Support and hoping for a fix soon 🤞

@PhoebeARice @art_egorov hm I can't see an issue at the moment. Which URL was causing the problem?

@PhoebeARice @art_egorov Oh interesting, sorry about that! Will look into it asap.

We now have representative seq blastp integrated into the new webFlaGs submission form made by @art_egorov, and it feels time to redirect webflags.se there! The classic page is still currently accessible at classic.webflags.se

If you have problems reaching the classic submission page today, try our new one instead server.atkinson-lab.com/webflags

Here we go! A network of toxin-antitoxins, AlphaFold-modelling of thousands of complexes, experimentally validation, and discoveries about TA neutralisation and relationships to phage defence systems on the way biorxiv.org/content/10.110… @Lundsuni @medfak_LU @KAWstiftelsen

The old webFlaGS submission system is getting through a queue after a crash. No better time to try our new server: server.atkinson-lab.com/webflags

@ditlevbrodersen @MacHomebrew Hi Ditlev! Nope, we don’t have that option. But give FlaGs2 installation a try and let us know how you get on. We can help if there’s a problem. github.com/GCA-VH-lab/Fla…