@webflags1

Status and examples from https://xitter.cf/t.co/0V6todXpX6, an Atkinson lab tool. Is your pet protein encoded in a conserved neighbourhood? 🚩🚩🏴‍☠️🚩🚩 Tweets by @gem__atkinson

 Umeå University
webflags.se
Joined May 2020
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  • Followers181
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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
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We had an issue with webFlaGs and uORF4u jobs getting stuck in the input validation step, but should be working fine now
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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-positio… You will be part of the new and exciting @scilifelab DDLS research school

PhD position available in high-throughput AlphaFold analyses of bacteriophage proteins

We are looking for a full-time bioinformatics PhD student to be involved in the DDLS project “Finding the prophages of Escherichia coli genomes and annotating the function of their genes usin…

atkinson-lab.com
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Please use this link to access webflags at the moment server.atkinson-lab.com/webf… Something up with the forwarding for the .se domain
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Hurray, we’ve fixed it! Webflags.se is taking submissions again!
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We're aware of some issue this weekend causing FlaGs to fail. Looking into it...
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local FlaGs2 seems unaffected
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The problem seems to be that we can't access @ncbi ftp.ncbi.nih.gov/ from Lund University servers
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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
Gene neighborhoods of rnpM across different organisms.

ALT Gene neighborhoods of rnpM across different organisms.

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Looks like the @NCBI protein database is a bit wobbly this morning. webFlaGs might be slow and/or submissions might fail.
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WebFlaGs retweeted
LU-Fold@LU_Fold8 Nov 2023
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/

LU-Fold: a protein structure prediction facility at Lund University

Welcome to LU-Fold! LU-Fold is a Lund University-based facility for helping researchers predict protein structures of interest using the cutting-edge method AlphaFold2 (Nature Methods method of the…

atkinson-lab.com
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That’s great to hear, thank you for the update!
NCBI@NCBI13 Sep 2023
Replying to @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].
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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'...
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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 🤞
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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
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If you have problems reaching the classic submission page today, try our new one instead server.atkinson-lab.com/webf…
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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/10.1101/… @Lundsuni @medfak_LU @KAWstiftelsen

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin...

Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode...

biorxiv.org
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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/webf…
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We're testing a new webFlaGs submission page and more stable queueing system made by PhD student @art_egorov. Give it a try and let us know what you think! server.atkinson-lab.com/webf…
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Excited to announce that through @art_egorov's hard work we have a server version of uORF4u for uORF/leader peptide prediction server.atkinson-lab.com/uorf… Artyom has also made a home page for the Atkinson lab tools, including his MSA4u alignment visualiser server.atkinson-lab.com/
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all better!
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