WebFlaGs

Status and examples from an Atkinson lab tool.
Is your pet protein encoded in a conserved neighbourhood?
🚩🚩🏴‍☠️🚩🚩
Tweets by @gem__atkinson

[WebFlaGs @webflags1]

We have a new feature of https://t.co/KNRVq5942p! 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

[WebFlaGs @webflags1]

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

[Gemma C Atkinson @gem__atkinson]

We are looking for a new PhD student to join us on our adventures in computational sequence and structural analyses of bacteriophage proteins https://t.co/PKqjxIIlT6
You will be part of the new and exciting @scilifelab DDLS research school

[WebFlaGs @webflags1]

Please use this link to access webflags at the moment https://t.co/WLV9JwYmY5 Something up with the forwarding for the .se domain

[WebFlaGs @webflags1]

Hurray, we’ve fixed it! https://t.co/AjUPYB39pS is taking submissions again!

[WebFlaGs @webflags1]

The problem seems to be that we can't access @ncbi https://t.co/ar0T4dky0Z from Lund University servers

[WebFlaGs @webflags1]

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

[WebFlaGs @webflags1]

local FlaGs2 seems unaffected

[Christoph Elfmann @c_elfmann]

An interactive visualization of conserved gene neighborhoods now on https://t.co/FtG39cj9Ja (#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

[WebFlaGs @webflags1]

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

[LU-Fold @LU_Fold]

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 https://t.co/MdpxL1HvhB

[WebFlaGs @webflags1]

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

[NCBI @NCBI]

@webflags1 Thank you for the report. We are working on the problem and hope to have it resolved soon. Sorry for the inconvenience and thank you for your patience! If you have questions, please contact our Help Desk at [email protected].

[WebFlaGs @webflags1]

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'...

[WebFlaGs @webflags1]

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 🤞

[WebFlaGs @webflags1]

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

[WebFlaGs @webflags1]

We now have representative seq blastp integrated into the new webFlaGs submission form made by @art_egorov, and it feels time to redirect https://t.co/0FlyWBImqv there! The classic page is still currently accessible at https://t.co/ZWqTElIi0W

[WebFlaGs @webflags1]

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

[WebFlaGs @webflags1]

If you have problems reaching the classic submission page today, try our new one instead https://t.co/WLV9JwYmY5

[Gemma C Atkinson @gem__atkinson]

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 https://t.co/iKCVO4oses @Lundsuni @medfak_LU @KAWstiftelsen

[WebFlaGs @webflags1]

The old webFlaGS submission system is getting through a queue after a crash. No better time to try our new server: https://t.co/WLV9JwYmY5

[WebFlaGs @webflags1]

@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. https://t.co/QUQ1sUQj1Z