Sally Cruikshank animates the difference between in and out. (The number of underground, avant garde artists I was was introduced to because of Sesame Street. This is why they want to take it away so hard.) www.youtube.com/watch?v=PGAP...
In and Out Crowd
YouTube video by Sally Cruikshank
www.youtube.com
May 6, 2025 at 8:44 PM
Sally Cruikshank animates the difference between in and out. (The number of underground, avant garde artists I was was introduced to because of Sesame Street. This is why they want to take it away so hard.) www.youtube.com/watch?v=PGAP...
Bakugou’s mouth drops open as he groans, his eyes shooting open as he looks down and up between Kirishima’s blown out pupils and the pgap between them, both of their panting only getting faster.
October 17, 2025 at 1:58 AM
Bakugou’s mouth drops open as he groans, his eyes shooting open as he looks down and up between Kirishima’s blown out pupils and the pgap between them, both of their panting only getting faster.
What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.
September 23, 2025 at 4:42 PM
What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
Now Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI Insights
Download release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...
ncbiinsights.ncbi.nlm.nih.gov
July 17, 2026 at 10:49 PM
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
First Play: Watch us play King of Meat, Amazon Games' comedy party platformer.
www.youtube.com/watch?v=pGAp...
www.youtube.com/watch?v=pGAp...
First Play: King of Meat (Xbox Series X)
YouTube video by VGC
www.youtube.com
October 2, 2025 at 5:08 PM
First Play: Watch us play King of Meat, Amazon Games' comedy party platformer.
www.youtube.com/watch?v=pGAp...
www.youtube.com/watch?v=pGAp...
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
October 4, 2025 at 6:31 PM
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
We have a bunch of MAGs sitting in GenBank queues for many months. I run all MAGs through PGAP so they’re BLAST-able & assigned accessions, which I refer to when discussing genes in MAGs in papers. This has ground to a halt w/ NCBI processing delays in recent years. Is there anyway to expedite this?
July 16, 2026 at 5:07 PM
We have a bunch of MAGs sitting in GenBank queues for many months. I run all MAGs through PGAP so they’re BLAST-able & assigned accessions, which I refer to when discussing genes in MAGs in papers. This has ground to a halt w/ NCBI processing delays in recent years. Is there anyway to expedite this?
Bao Got Scammed with Labubus
YouTube video by Bao The Whale
www.youtube.com
September 25, 2025 at 4:37 PM
We’ve found the annotations from PGAP much more useful than polls, been meaning to try bakta but haven’t. PGAP is a huge pain to try running locally though.
October 5, 2025 at 6:18 PM
We’ve found the annotations from PGAP much more useful than polls, been meaning to try bakta but haven’t. PGAP is a huge pain to try running locally though.
Hi, joined blue sky today. Finished work for the day and seem to be over my cr*pgap this month. On kesimpta for 2yrs and suddenly developed medication wearing off symptoms in last 2 months. It’s been a nightmare. Raring to go for the weekend. A good day all round
day.as
August 9, 2024 at 2:35 PM
Hi, joined blue sky today. Finished work for the day and seem to be over my cr*pgap this month. On kesimpta for 2yrs and suddenly developed medication wearing off symptoms in last 2 months. It’s been a nightmare. Raring to go for the weekend. A good day all round
✨ Lace meets mesh in all the right ways! ✨ Elevate your look with this Lace Mesh Long Sleeve Top — sheer elegance + subtle detail. Perfect for layering, date nights, or just when you want to feel effortlessly chic. 🛍️ Check it out → go.live365days.com/pGap #MeshTop #Fashion #StyleDetails 💃🕺💅
September 23, 2025 at 1:09 AM
✨ Lace meets mesh in all the right ways! ✨ Elevate your look with this Lace Mesh Long Sleeve Top — sheer elegance + subtle detail. Perfect for layering, date nights, or just when you want to feel effortlessly chic. 🛍️ Check it out → go.live365days.com/pGap #MeshTop #Fashion #StyleDetails 💃🕺💅
We have just stumbled across potential gene calling issues in PKS genes with PGAP 6.8 in RefSeq sequences. It looks like that PGAP version adds random stops in the middle of ORFs, splitting genes into small parts. If you have suspicious looking fragments, try running the FASTA file in antiSMASH
January 16, 2025 at 3:01 PM
We have just stumbled across potential gene calling issues in PKS genes with PGAP 6.8 in RefSeq sequences. It looks like that PGAP version adds random stops in the middle of ORFs, splitting genes into small parts. If you have suspicious looking fragments, try running the FASTA file in antiSMASH
Worth a listen:
“Beyond the Petri Dish”
Interview with #GeorgeTsakraklides, hosted by #MichaelBayliss and #MarkAllen of #PGAP (Post-Growth Australia Podcast)
#TalkCollapse
“Beyond the Petri Dish”
Interview with #GeorgeTsakraklides, hosted by #MichaelBayliss and #MarkAllen of #PGAP (Post-Growth Australia Podcast)
#TalkCollapse
Beyond the Petri Dish with George Tsakraklides
In this latest episode we speak with scientist, researcher, and author George Tsakraklides about the deeper roots of humanity’s many crises. Drawing on his rich scientific background and corporate ins...
pgap.fireside.fm
May 13, 2025 at 12:44 AM
Worth a listen:
“Beyond the Petri Dish”
Interview with #GeorgeTsakraklides, hosted by #MichaelBayliss and #MarkAllen of #PGAP (Post-Growth Australia Podcast)
#TalkCollapse
“Beyond the Petri Dish”
Interview with #GeorgeTsakraklides, hosted by #MichaelBayliss and #MarkAllen of #PGAP (Post-Growth Australia Podcast)
#TalkCollapse
Really tried to reduce my profanity, but this is a cluster fuck!
With AmeriKa giving away our mutual security, threatening Greenland, Panama, Ukraine, Gaza & Canada with annexation, there is ZERO possibility of them delivering ONE sub.
Another $18 billion? No! AmeriKa OUT of 5 Eyes PGap & AUKUS!
With AmeriKa giving away our mutual security, threatening Greenland, Panama, Ukraine, Gaza & Canada with annexation, there is ZERO possibility of them delivering ONE sub.
Another $18 billion? No! AmeriKa OUT of 5 Eyes PGap & AUKUS!
March 26, 2025 at 6:41 AM
Really tried to reduce my profanity, but this is a cluster fuck!
With AmeriKa giving away our mutual security, threatening Greenland, Panama, Ukraine, Gaza & Canada with annexation, there is ZERO possibility of them delivering ONE sub.
Another $18 billion? No! AmeriKa OUT of 5 Eyes PGap & AUKUS!
With AmeriKa giving away our mutual security, threatening Greenland, Panama, Ukraine, Gaza & Canada with annexation, there is ZERO possibility of them delivering ONE sub.
Another $18 billion? No! AmeriKa OUT of 5 Eyes PGap & AUKUS!
Just want to follow up that I implemented steps using some of your filtering advice, autocycler and recommended post steps, and pgap for annotation and it worked great. Thanks for your help.
July 11, 2025 at 10:33 AM
Just want to follow up that I implemented steps using some of your filtering advice, autocycler and recommended post steps, and pgap for annotation and it worked great. Thanks for your help.
Last month couldn’t walk 3 days before/after injection. This month not so bad but tripping and fell over couple of times. Consultant thinks each month will be better than previous month but could take 6 months to pass. Having an MRI to double check. I didn’t realise cr*pgap with Kesimpta either
August 9, 2024 at 2:44 PM
Last month couldn’t walk 3 days before/after injection. This month not so bad but tripping and fell over couple of times. Consultant thinks each month will be better than previous month but could take 6 months to pass. Having an MRI to double check. I didn’t realise cr*pgap with Kesimpta either
Michael Bayliss and Mark Allen explore lived experience, poetry, planning and shifting baselines in A Journey Through #Solastalgia.
Listen: pgap.fireside.fm/solastalgia
#PGAP explores post growth futures and is supported by SPA.
#LiveWithinLimits #SustainablePopulationAustralia #PostGrowthAustralia
Listen: pgap.fireside.fm/solastalgia
#PGAP explores post growth futures and is supported by SPA.
#LiveWithinLimits #SustainablePopulationAustralia #PostGrowthAustralia
August 16, 2026 at 6:04 AM
Michael Bayliss and Mark Allen explore lived experience, poetry, planning and shifting baselines in A Journey Through #Solastalgia.
Listen: pgap.fireside.fm/solastalgia
#PGAP explores post growth futures and is supported by SPA.
#LiveWithinLimits #SustainablePopulationAustralia #PostGrowthAustralia
Listen: pgap.fireside.fm/solastalgia
#PGAP explores post growth futures and is supported by SPA.
#LiveWithinLimits #SustainablePopulationAustralia #PostGrowthAustralia
Large-scale benchmarking of prokaryotic annotation tools across thousands of species | Genome Biology | Springer Nature Link
Large-scale benchmarking of prokaryotic annotation tools across thousands of species - Genome Biology
Background Genome annotation is an important step in deriving functional meaning from prokaryotic sequencing data, yet systematic evaluations guiding tool selection are lacking. We present the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes. This includes Escherichia coli strains for baseline performance, thousands of archaea and bacteria genomes, as well as frameshifted and metagenome-assembled genomes. Results Bakta excels in annotating high-quality bacterial genomes, while PGAP was better for archaeal genomes and challenging bacterial assemblies, including metagenome-assembled, fragmented, or contaminated samples. For Gene Ontology annotation, PGAP consistently provides broader term coverage, whereas EggNOG-mapper offers more terms per feature. Conclusions Our findings highlight tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin (e.g. MAGs). This study provides an evidence-based guide for users and informs future tool development.
link.springer.com
September 5, 2026 at 3:20 AM
Large-scale benchmarking of prokaryotic annotation tools across thousands of species | Genome Biology | Springer Nature Link
Check out my interview with Michael Bayliss on the Post-Growth Australia Podcast. We discuss Big Tech's humachination agenda, the dangers of unregulated AI & robotics, the perils of Smartheid surveillance and the incomparably better future degrowth society can offer.
pgap.fireside.fm/humachines
pgap.fireside.fm/humachines
Techno Dystopia and the Age of Humachines with Michael D.B. Harvey
In this episode of PGAP, we’re joined by Michael D.B. Harvey, author of The Age of Humachines: Big Tech and the Battle for Humanity’s Future. Harvey offers a sobering perspective on the trajectory of ...
pgap.fireside.fm
July 1, 2025 at 10:45 AM
Check out my interview with Michael Bayliss on the Post-Growth Australia Podcast. We discuss Big Tech's humachination agenda, the dangers of unregulated AI & robotics, the perils of Smartheid surveillance and the incomparably better future degrowth society can offer.
pgap.fireside.fm/humachines
pgap.fireside.fm/humachines
In late 2024, we proudly welcomed Professor Anne Poelina as our newest Patron.
This mini-podcast episode features the audio recording from a video interview that co-host Michael Bayliss conducted with Anne as part of SPA's "Meet the Patrons" series.
pgap.fireside.fm/annepoelinap...
This mini-podcast episode features the audio recording from a video interview that co-host Michael Bayliss conducted with Anne as part of SPA's "Meet the Patrons" series.
pgap.fireside.fm/annepoelinap...
PGAP Welcomes Back Anne Poelina New Patron of SPA
In late 2024, Sustainable Population Australia (SPA) proudly welcomed Professor Anne Poelina as its newest Patron. This mini-episode features the audio recording from a video interview that co-host Mi...
pgap.fireside.fm
January 22, 2025 at 6:02 AM
In late 2024, we proudly welcomed Professor Anne Poelina as our newest Patron.
This mini-podcast episode features the audio recording from a video interview that co-host Michael Bayliss conducted with Anne as part of SPA's "Meet the Patrons" series.
pgap.fireside.fm/annepoelinap...
This mini-podcast episode features the audio recording from a video interview that co-host Michael Bayliss conducted with Anne as part of SPA's "Meet the Patrons" series.
pgap.fireside.fm/annepoelinap...
We have solutions already; the difficulty isn't finding solutions, it's getting them implemented.
On that note, I enjoyed this recent podcast on implementing citizens assemblies: pgap.fireside.fm/capad
Apple Podcast link to the episode: podcasts.apple.com/nl/podcast/p...
On that note, I enjoyed this recent podcast on implementing citizens assemblies: pgap.fireside.fm/capad
Apple Podcast link to the episode: podcasts.apple.com/nl/podcast/p...
Citizen Assemblies for a Democratic, Post-Growth Future with Peter Tait
In this episode of PGAP, host Michael Bayliss welcomes special guest Peter Tait, convenor of the Canberra Alliance for Participatory Democracy. Peter discusses the critical importance of citizen part...
pgap.fireside.fm
May 8, 2026 at 1:22 PM
We have solutions already; the difficulty isn't finding solutions, it's getting them implemented.
On that note, I enjoyed this recent podcast on implementing citizens assemblies: pgap.fireside.fm/capad
Apple Podcast link to the episode: podcasts.apple.com/nl/podcast/p...
On that note, I enjoyed this recent podcast on implementing citizens assemblies: pgap.fireside.fm/capad
Apple Podcast link to the episode: podcasts.apple.com/nl/podcast/p...
But things change when genome quality becomes more challenging. For #MAGs, fragmented assemblies and genomes affected by sequencing errors/frameshifts, PGAP showed greater robustness, maintaining more consistent coding density and feature counts.
Achaea: PGAP was also the strongest overall option.
Achaea: PGAP was also the strongest overall option.
September 13, 2026 at 3:37 PM
But things change when genome quality becomes more challenging. For #MAGs, fragmented assemblies and genomes affected by sequencing errors/frameshifts, PGAP showed greater robustness, maintaining more consistent coding density and feature counts.
Achaea: PGAP was also the strongest overall option.
Achaea: PGAP was also the strongest overall option.