HMMER, Pfam, and Rfam are critical to so many Bioinformatics pipelines. This is absolutely crazy
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
www.npr.org
May 26, 2026 at 3:34 PM
HMMER, Pfam, and Rfam are critical to so many Bioinformatics pipelines. This is absolutely crazy
This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.
May 29, 2025 at 7:00 AM
This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.
The Baker lab seems serious about moving into enzyme design.
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
November 15, 2024 at 10:11 PM
The Baker lab seems serious about moving into enzyme design.
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
The data can be explored interactively at bioi2.i2bc.paris-saclay.fr/django/rnapr...
thanks to the #I2BC bioinformatics facility
thanks to the #I2BC bioinformatics facility
RNAprotDBgroup1
ECOD arch-name: a+b two layers; a/b three-layered sandwiches
RFAM family: tRNA
RFAM clan: tRNA clan
Ribosome? no
Group size: 2group2
ECOD arch-name: a+b two layers
RFAM family:
RFAM c...
bioi2.i2bc.paris-saclay.fr
December 3, 2024 at 10:03 PM
The data can be explored interactively at bioi2.i2bc.paris-saclay.fr/django/rnapr...
thanks to the #I2BC bioinformatics facility
thanks to the #I2BC bioinformatics facility
We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 17, 2025 at 5:10 PM
We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
RNA3DB 2025-10-01 release
github.com/marcellszi/r...
#RNA #RNAsky
The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation.
More chains (25,666), more independent components (144), more Rfam families represented (853).
github.com/marcellszi/r...
#RNA #RNAsky
The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation.
More chains (25,666), more independent components (144), more Rfam families represented (853).
October 10, 2025 at 3:51 PM
RNA3DB 2025-10-01 release
github.com/marcellszi/r...
#RNA #RNAsky
The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation.
More chains (25,666), more independent components (144), more Rfam families represented (853).
github.com/marcellszi/r...
#RNA #RNAsky
The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation.
More chains (25,666), more independent components (144), more Rfam families represented (853).
New webinar:
Accessing RNA data programmatically with the Rfam and RNAcentral APIs
📅 Thursday 25 June 2026, 14:30–15:30 (BST)
🔗 Registration is free but essential:
www.ebi.ac.uk/training/eve...
@rnacentral.bsky.social @rfamdb.bsky.social
#bioinformatics #ncRNA
Accessing RNA data programmatically with the Rfam and RNAcentral APIs
📅 Thursday 25 June 2026, 14:30–15:30 (BST)
🔗 Registration is free but essential:
www.ebi.ac.uk/training/eve...
@rnacentral.bsky.social @rfamdb.bsky.social
#bioinformatics #ncRNA
Accessing RNA data programmatically with the Rfam and RNAcentral APIs -
Accessing RNA data programmatically with the Rfam and RNAcentral APIs -
www.ebi.ac.uk
May 15, 2026 at 5:17 PM
New webinar:
Accessing RNA data programmatically with the Rfam and RNAcentral APIs
📅 Thursday 25 June 2026, 14:30–15:30 (BST)
🔗 Registration is free but essential:
www.ebi.ac.uk/training/eve...
@rnacentral.bsky.social @rfamdb.bsky.social
#bioinformatics #ncRNA
Accessing RNA data programmatically with the Rfam and RNAcentral APIs
📅 Thursday 25 June 2026, 14:30–15:30 (BST)
🔗 Registration is free but essential:
www.ebi.ac.uk/training/eve...
@rnacentral.bsky.social @rfamdb.bsky.social
#bioinformatics #ncRNA
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
www.npr.org
May 25, 2026 at 5:53 PM
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
"had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
An opportunity to run the greatest little RNA Databases that can, Rfam & RNAcentral: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
The only downside is you have to live near Cambridge in the UK.
The only downside is you have to live near Cambridge in the UK.
RNA Resources Project Leader
About the team/job We are recruiting a Project Leader to spearhead the development of the RNAcentral and Rfam databases. Rfam and RNAcentral are key resources for RNA Biology that serve tens of thousa...
embl.wd103.myworkdayjobs.com
June 6, 2025 at 7:30 AM
An opportunity to run the greatest little RNA Databases that can, Rfam & RNAcentral: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
The only downside is you have to live near Cambridge in the UK.
The only downside is you have to live near Cambridge in the UK.
Ik ben niet vaak trots op Rob Jetten; het is niet dat hij nou écht iets maakt van zijn rol, maar deze speech, daar ben ik apetrots op. Rob heeft ballen!
www.youtube.com/watch?v=RFAm...
www.youtube.com/watch?v=RFAm...
“Hands Off the ICC”, Dutch PM Defends ICC, Slams Attacks on Global Justice in Fiery UN Speech | AC1G
YouTube video by DRM News
www.youtube.com
September 25, 2026 at 7:53 AM
Ik ben niet vaak trots op Rob Jetten; het is niet dat hij nou écht iets maakt van zijn rol, maar deze speech, daar ben ik apetrots op. Rob heeft ballen!
www.youtube.com/watch?v=RFAm...
www.youtube.com/watch?v=RFAm...
Looking forward to speaking about Rfam and RNAcentral at the Cambridge RNA Club!
From Bolivia to Oxford, Nanopore, and York!
Don't miss our next RNA Club this Thursday 28th at 16:30! We are thrilled to host Miguel Aracena. He will break down his PhD work on the mechanistic basis for translation initiation on enterovirus IRES.
@cambiochem.bsky.social @york.ac.uk
Don't miss our next RNA Club this Thursday 28th at 16:30! We are thrilled to host Miguel Aracena. He will break down his PhD work on the mechanistic basis for translation initiation on enterovirus IRES.
@cambiochem.bsky.social @york.ac.uk
May 26, 2026 at 4:47 PM
Looking forward to speaking about Rfam and RNAcentral at the Cambridge RNA Club!
📢 Rfam 15.1 is here!
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
January 28, 2026 at 11:16 AM
📢 Rfam 15.1 is here!
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
Meet SQUARNA 3.0, our tool for #RNA secondary structure prediction:
pypi.org/project/SQUA...
Now with options for @rfamdb.bsky.social Rfam template search and G-quadruplex pattern recognition!
Currently, as CLI and Python API, and soon, a web version.
#Rfam #G4 #Gquadruplex #Bioinformatics
pypi.org/project/SQUA...
Now with options for @rfamdb.bsky.social Rfam template search and G-quadruplex pattern recognition!
Currently, as CLI and Python API, and soon, a web version.
#Rfam #G4 #Gquadruplex #Bioinformatics
February 18, 2026 at 12:28 PM
Meet SQUARNA 3.0, our tool for #RNA secondary structure prediction:
pypi.org/project/SQUA...
Now with options for @rfamdb.bsky.social Rfam template search and G-quadruplex pattern recognition!
Currently, as CLI and Python API, and soon, a web version.
#Rfam #G4 #Gquadruplex #Bioinformatics
pypi.org/project/SQUA...
Now with options for @rfamdb.bsky.social Rfam template search and G-quadruplex pattern recognition!
Currently, as CLI and Python API, and soon, a web version.
#Rfam #G4 #Gquadruplex #Bioinformatics
Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT https://www.biorxiv.org/content/10.64898/2026.05.10.724034v1
May 14, 2026 at 5:47 PM
Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT https://www.biorxiv.org/content/10.64898/2026.05.10.724034v1
SeqHub now surfaces Rfam annotations directly in the genomic neighborhood view: family name, accession, length, and a link out to the Rfam entry.
March 31, 2026 at 5:25 PM
SeqHub now surfaces Rfam annotations directly in the genomic neighborhood view: family name, accession, length, and a link out to the Rfam entry.
Major spliceosomal RNA secondary structures, interactions (PDB), evolutionary conservation (PhyloP & Rfam SEEDs), and disease associations (D’Souza et al 2026). All in one monstrously busy plot. 😁
August 31, 2026 at 10:20 PM
Major spliceosomal RNA secondary structures, interactions (PDB), evolutionary conservation (PhyloP & Rfam SEEDs), and disease associations (D’Souza et al 2026). All in one monstrously busy plot. 😁
Search for known loop motif 3D structures in Rfam with JAR3D bit.ly/41ctfEQ
July 10, 2026 at 5:02 PM
Search for known loop motif 3D structures in Rfam with JAR3D bit.ly/41ctfEQ
Join us on 25 June 2026 for our free webinar 'Accessing RNA data programmatically with the Rfam and RNAcentral APIs': www.ebi.ac.uk/training/eve...
Registration is free but essential to secure your place.
Speakers: Isaac Jandalala and Philippa Muston, Full Stack Developers at @ebi.embl.org
🖥️🧬📊
Registration is free but essential to secure your place.
Speakers: Isaac Jandalala and Philippa Muston, Full Stack Developers at @ebi.embl.org
🖥️🧬📊
June 16, 2026 at 10:57 AM
Join us on 25 June 2026 for our free webinar 'Accessing RNA data programmatically with the Rfam and RNAcentral APIs': www.ebi.ac.uk/training/eve...
Registration is free but essential to secure your place.
Speakers: Isaac Jandalala and Philippa Muston, Full Stack Developers at @ebi.embl.org
🖥️🧬📊
Registration is free but essential to secure your place.
Speakers: Isaac Jandalala and Philippa Muston, Full Stack Developers at @ebi.embl.org
🖥️🧬📊
3/ Repeat masking baked in. Evidence types first-class: RNA-Seq, PacBio IsoSeq (BAM/FASTQ), proteins, plus a dual mode fusing all three. VARUS pulls SRA from just genus + species. UTRs via StringTie2. Optional ncRNA: rRNA, tRNA, Rfam, lncRNA merged into one GFF3.
April 11, 2026 at 7:12 PM
3/ Repeat masking baked in. Evidence types first-class: RNA-Seq, PacBio IsoSeq (BAM/FASTQ), proteins, plus a dual mode fusing all three. VARUS pulls SRA from just genus + species. UTRs via StringTie2. Optional ncRNA: rRNA, tRNA, Rfam, lncRNA merged into one GFF3.
In Pseudomonas, the TwoAYGGAY RNA family extends well past its Rfam annotation, with three further hairpins and a 3’ pseudoknot on an elongated basal stem. A covariance model rebuilt on the Minerva predictions found 16,086 matches across 1,148 of 1,324 strains.
September 23, 2026 at 5:21 PM
In Pseudomonas, the TwoAYGGAY RNA family extends well past its Rfam annotation, with three further hairpins and a 3’ pseudoknot on an elongated basal stem. A covariance model rebuilt on the Minerva predictions found 16,086 matches across 1,148 of 1,324 strains.
🚀 We're hiring a 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 𝗗𝗮𝘁𝗮 𝗘𝗻𝗴𝗶𝗻𝗲𝗲𝗿 to run, maintain and optimise pipelines behind Rfam and RNAcentral, including development of LLMs, agent orchestration workflows, and more!
Apply by 28 June👇 embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
#RNA #Bioinformatics #AI #DataEngineering #job
Apply by 28 June👇 embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
#RNA #Bioinformatics #AI #DataEngineering #job
Bioinformatics Data Engineer (RNA Resources)
About the Team Rfam and RNAcentral are key resources for RNA biology, serving tens of thousands of users every year and widely cited in the scientific literature. We are recruiting a Bioinformatics Da...
embl.wd103.myworkdayjobs.com
June 1, 2026 at 8:27 PM
🚀 We're hiring a 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 𝗗𝗮𝘁𝗮 𝗘𝗻𝗴𝗶𝗻𝗲𝗲𝗿 to run, maintain and optimise pipelines behind Rfam and RNAcentral, including development of LLMs, agent orchestration workflows, and more!
Apply by 28 June👇 embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
#RNA #Bioinformatics #AI #DataEngineering #job
Apply by 28 June👇 embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
#RNA #Bioinformatics #AI #DataEngineering #job
Rfam 15.0 brings expanded genomes, improved RNA annotations, & new data types for advanced RNA research. Check out the latest updates! 🌟 #Bioinformatics #RNAresearch #GenomeAnnotation
📄 doi.org/10.1093/nar/...
EVBC👤: Sandra Triebel, Manja Marz
📄 doi.org/10.1093/nar/...
EVBC👤: Sandra Triebel, Manja Marz
Rfam 15: RNA families database in 2025
Abstract. The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces
doi.org
December 3, 2024 at 1:49 PM
Rfam 15.0 brings expanded genomes, improved RNA annotations, & new data types for advanced RNA research. Check out the latest updates! 🌟 #Bioinformatics #RNAresearch #GenomeAnnotation
📄 doi.org/10.1093/nar/...
EVBC👤: Sandra Triebel, Manja Marz
📄 doi.org/10.1093/nar/...
EVBC👤: Sandra Triebel, Manja Marz
Random Fact About Me (RFAM)-
When I am singing a song and don't know a word or seven, I just just replace each syllable with "meow"
Try it!
#randomfactaboutme
When I am singing a song and don't know a word or seven, I just just replace each syllable with "meow"
Try it!
#randomfactaboutme
February 7, 2025 at 7:01 PM
Random Fact About Me (RFAM)-
When I am singing a song and don't know a word or seven, I just just replace each syllable with "meow"
Try it!
#randomfactaboutme
When I am singing a song and don't know a word or seven, I just just replace each syllable with "meow"
Try it!
#randomfactaboutme