Curious, if someone wanted to annotate a large set of MAGs with KEGG, PFAM, CAZY, and then do some statistical comparison, how would you do that these days?
Back in the day I loved EnrichM, but the backend databases for KEGG, etc, are woefully out of date now.
Back in the day I loved EnrichM, but the backend databases for KEGG, etc, are woefully out of date now.
October 6, 2025 at 5:18 PM
Curious, if someone wanted to annotate a large set of MAGs with KEGG, PFAM, CAZY, and then do some statistical comparison, how would you do that these days?
Back in the day I loved EnrichM, but the backend databases for KEGG, etc, are woefully out of date now.
Back in the day I loved EnrichM, but the backend databases for KEGG, etc, are woefully out of date now.
🆕 New version of InterProScan: 5.73-104.0
3 ways to use it:
1️⃣ Sequence search on the InterPro website: ebi.ac.uk/interpro/sea...
2️⃣ Local installation: interproscan-docs.readthedocs.io/en/v5/Instal...
3️⃣ Local installation using a container: interproscan-docs.readthedocs.io/en/v5/HowToU...
💻🧪
3 ways to use it:
1️⃣ Sequence search on the InterPro website: ebi.ac.uk/interpro/sea...
2️⃣ Local installation: interproscan-docs.readthedocs.io/en/v5/Instal...
3️⃣ Local installation using a container: interproscan-docs.readthedocs.io/en/v5/HowToU...
💻🧪
February 25, 2025 at 11:22 AM
🆕 New version of InterProScan: 5.73-104.0
3 ways to use it:
1️⃣ Sequence search on the InterPro website: ebi.ac.uk/interpro/sea...
2️⃣ Local installation: interproscan-docs.readthedocs.io/en/v5/Instal...
3️⃣ Local installation using a container: interproscan-docs.readthedocs.io/en/v5/HowToU...
💻🧪
3 ways to use it:
1️⃣ Sequence search on the InterPro website: ebi.ac.uk/interpro/sea...
2️⃣ Local installation: interproscan-docs.readthedocs.io/en/v5/Instal...
3️⃣ Local installation using a container: interproscan-docs.readthedocs.io/en/v5/HowToU...
💻🧪
InterPro release 103.0 is live! 💻🧪
✨Update to Pfam 37.1
✨1029 new entries, including 1019 signatures from the Pfam (1008), NCBIfam (2), PIRSF (1), PANTHER (1), CDD (7) databases.
Have a look: ebi.ac.uk/interpro/
✨Update to Pfam 37.1
✨1029 new entries, including 1019 signatures from the Pfam (1008), NCBIfam (2), PIRSF (1), PANTHER (1), CDD (7) databases.
Have a look: ebi.ac.uk/interpro/
November 29, 2024 at 8:29 AM
InterPro release 103.0 is live! 💻🧪
✨Update to Pfam 37.1
✨1029 new entries, including 1019 signatures from the Pfam (1008), NCBIfam (2), PIRSF (1), PANTHER (1), CDD (7) databases.
Have a look: ebi.ac.uk/interpro/
✨Update to Pfam 37.1
✨1029 new entries, including 1019 signatures from the Pfam (1008), NCBIfam (2), PIRSF (1), PANTHER (1), CDD (7) databases.
Have a look: ebi.ac.uk/interpro/
📆 la #cyberattaque revendiquée le 28 mai 2024 (qilin) contre 🇺🇸 PFAM (precisionflange.com) semble survenue ~11 mai 2024 🧐https://www.ransomware.live/#/recentcyberattacks
July 10, 2024 at 4:55 PM
📆 la #cyberattaque revendiquée le 28 mai 2024 (qilin) contre 🇺🇸 PFAM (precisionflange.com) semble survenue ~11 mai 2024 🧐https://www.ransomware.live/#/recentcyberattacks
I don't know much about that database, but you could download hmm profiles from PFAM if you know the PFAM ID of a particular enzyme/protein. Example: HMM of pectate lyase can be found here:
www.ebi.ac.uk/interpro/ent...
www.ebi.ac.uk/interpro/ent...
October 12, 2023 at 3:32 PM
I don't know much about that database, but you could download hmm profiles from PFAM if you know the PFAM ID of a particular enzyme/protein. Example: HMM of pectate lyase can be found here:
www.ebi.ac.uk/interpro/ent...
www.ebi.ac.uk/interpro/ent...
Authors published a paper in Biorxiv, they used Pfam in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
www.biorxiv.org
October 2, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used Pfam in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
Like 9:
Fake Meat Must Die (Hotdogs, Horseshoes, and Handgrenades)
Whilst I may not use this song often in a typical Take and Hold Run, I still like the gamemode overall (and the music)
www.youtube.com/watch?v=pFAM...
Fake Meat Must Die (Hotdogs, Horseshoes, and Handgrenades)
Whilst I may not use this song often in a typical Take and Hold Run, I still like the gamemode overall (and the music)
www.youtube.com/watch?v=pFAM...
H3VR OST: Take and Hold Combat Music - Fake Meat Must Die
YouTube video by Anton Hand
www.youtube.com
December 3, 2024 at 12:03 AM
Like 9:
Fake Meat Must Die (Hotdogs, Horseshoes, and Handgrenades)
Whilst I may not use this song often in a typical Take and Hold Run, I still like the gamemode overall (and the music)
www.youtube.com/watch?v=pFAM...
Fake Meat Must Die (Hotdogs, Horseshoes, and Handgrenades)
Whilst I may not use this song often in a typical Take and Hold Run, I still like the gamemode overall (and the music)
www.youtube.com/watch?v=pFAM...
Our latest work has been published in #Bioinformatics Advances ProCogGraph, the spiritual successor of PROCOGNATE. This graph database provides a linkage between proteins domains (SCOP/CATH/Pfam) and cognate ligands for #enzymes in the #PDB. academic.oup.com/bioinformati...
ProCogGraph: a graph-based mapping of cognate ligand domain interactions
AbstractMotivation. Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docki
academic.oup.com
November 14, 2024 at 7:56 PM
Our latest work has been published in #Bioinformatics Advances ProCogGraph, the spiritual successor of PROCOGNATE. This graph database provides a linkage between proteins domains (SCOP/CATH/Pfam) and cognate ligands for #enzymes in the #PDB. academic.oup.com/bioinformati...
December version of @hmm3r released! New: Pfam (@Xfam_EBI) 📍active sites📍 now included in the searches. Try it now @ https://www.ebi.ac.uk/Tools/hmmer/
March 31, 2025 at 10:21 AM
December version of @hmm3r released! New: Pfam (@Xfam_EBI) 📍active sites📍 now included in the searches. Try it now @ https://www.ebi.ac.uk/Tools/hmmer/
📢InterPro release 105.0 is live!
✨Update to Pfam 37.3, PROSITE patterns 2025_01
PROSITE profiles 2025_01 and HAMAP 2025_01
✨342 new entries
✨Addition of InterPro-N annotations
✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab
Have a look: ebi.ac.uk/interpro/htt...
💻🧪🆕
✨Update to Pfam 37.3, PROSITE patterns 2025_01
PROSITE profiles 2025_01 and HAMAP 2025_01
✨342 new entries
✨Addition of InterPro-N annotations
✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab
Have a look: ebi.ac.uk/interpro/htt...
💻🧪🆕
April 24, 2025 at 4:07 PM
📢InterPro release 105.0 is live!
✨Update to Pfam 37.3, PROSITE patterns 2025_01
PROSITE profiles 2025_01 and HAMAP 2025_01
✨342 new entries
✨Addition of InterPro-N annotations
✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab
Have a look: ebi.ac.uk/interpro/htt...
💻🧪🆕
✨Update to Pfam 37.3, PROSITE patterns 2025_01
PROSITE profiles 2025_01 and HAMAP 2025_01
✨342 new entries
✨Addition of InterPro-N annotations
✨Addition of BFVD structure predictions from @martinsteinegger.bsky.social's lab
Have a look: ebi.ac.uk/interpro/htt...
💻🧪🆕
ET-Pfam: Ensemble transfer learning for protein family prediction
doi.org/10.1101/2025...
Automatic annotation of the bHLH gene family in plants
doi.org/10.1101/2023...
#Bioinformatics #DataScience #GeneFamily
doi.org/10.1101/2025...
Automatic annotation of the bHLH gene family in plants
doi.org/10.1101/2023...
#Bioinformatics #DataScience #GeneFamily
doi.org
September 4, 2025 at 4:16 AM
ET-Pfam: Ensemble transfer learning for protein family prediction
doi.org/10.1101/2025...
Automatic annotation of the bHLH gene family in plants
doi.org/10.1101/2023...
#Bioinformatics #DataScience #GeneFamily
doi.org/10.1101/2025...
Automatic annotation of the bHLH gene family in plants
doi.org/10.1101/2023...
#Bioinformatics #DataScience #GeneFamily
Pfam are on here!
For the latest Pfam updates, have a look at our recently published paper: The Pfam protein families database: embracing AI/ML
t.co/8auCxw3mdj
t.co/8auCxw3mdj
November 30, 2024 at 8:24 AM
Pfam are on here!
For DCD, the Principal:2 isoform was the isoform with the intact Pfam domain. Unfortunately, the Pfam domain was based on erroneous transcript predictions in primates.
Structure and function is known for the 110 aa protein (Principal:M), while the 121 aa protein (Alternative:M) is uninteresting.
Structure and function is known for the 110 aa protein (Principal:M), while the 121 aa protein (Alternative:M) is uninteresting.
February 24, 2025 at 12:33 PM
For DCD, the Principal:2 isoform was the isoform with the intact Pfam domain. Unfortunately, the Pfam domain was based on erroneous transcript predictions in primates.
Structure and function is known for the 110 aa protein (Principal:M), while the 121 aa protein (Alternative:M) is uninteresting.
Structure and function is known for the 110 aa protein (Principal:M), while the 121 aa protein (Alternative:M) is uninteresting.
New preprint alert: We define two new metrics V-score and VL-score for genomes and protein families with applications in viral genomics and ecology. These metrics for KEGG, Pfam, eggNOG, VOG, PHROG, are publicly available-https://anantharamanlab.github.io/V-Score-Search/.
biorxiv.org/cgi/content/...
biorxiv.org/cgi/content/...
V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families
Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which fo...
biorxiv.org
October 30, 2024 at 2:12 AM
New preprint alert: We define two new metrics V-score and VL-score for genomes and protein families with applications in viral genomics and ecology. These metrics for KEGG, Pfam, eggNOG, VOG, PHROG, are publicly available-https://anantharamanlab.github.io/V-Score-Search/.
biorxiv.org/cgi/content/...
biorxiv.org/cgi/content/...
I have been trying to onboard the 2A peptide pHMM models into Pfam to no avail. If anyone has a contact there, I would appreciate an introduction for a discussion.
github.com/rnabioco/2a-...
github.com/rnabioco/2a-...
GitHub - rnabioco/2a-peptide-search: HMM models of the 2A peptide and DB search results
HMM models of the 2A peptide and DB search results - rnabioco/2a-peptide-search
github.com
June 20, 2025 at 12:27 AM
I have been trying to onboard the 2A peptide pHMM models into Pfam to no avail. If anyone has a contact there, I would appreciate an introduction for a discussion.
github.com/rnabioco/2a-...
github.com/rnabioco/2a-...
We identified:
3,000+ enriched Pfam domains
16,000+ enriched AlphaFold clusters
1,500+ operons enriched in host-associated bacteria
🧬 Many with no known function—yet strongly conserved across taxa
3,000+ enriched Pfam domains
16,000+ enriched AlphaFold clusters
1,500+ operons enriched in host-associated bacteria
🧬 Many with no known function—yet strongly conserved across taxa
July 21, 2025 at 6:40 AM
We identified:
3,000+ enriched Pfam domains
16,000+ enriched AlphaFold clusters
1,500+ operons enriched in host-associated bacteria
🧬 Many with no known function—yet strongly conserved across taxa
3,000+ enriched Pfam domains
16,000+ enriched AlphaFold clusters
1,500+ operons enriched in host-associated bacteria
🧬 Many with no known function—yet strongly conserved across taxa
Authors published a paper in #BioRxiv, they used Pfam in the study. Including #RRIDs will make this less ambiguous.
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
Comparative genomics of sex determination related genes reveals shared evolutionary patterns between bivalves and mammals, but not Drosophila
www.biorxiv.org
February 13, 2025 at 12:23 AM
Authors published a paper in #BioRxiv, they used Pfam in the study. Including #RRIDs will make this less ambiguous.
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
🔍 Lost in Pfam data? Our redesigned Help page has you covered! From quick answers to deep dives into protein families, find exactly what you need at www.ebi.ac.uk/interpro/help/ 💻🧪
January 24, 2025 at 11:04 AM
🔍 Lost in Pfam data? Our redesigned Help page has you covered! From quick answers to deep dives into protein families, find exactly what you need at www.ebi.ac.uk/interpro/help/ 💻🧪
📣 A new version of InterProScan (5.72-103.0) is available. You can download it here: ebi.ac.uk/interpro/abo... More info and documentation: interproscan-docs.readthedocs.io/en/latest/Re...
🧪💻🧬
🧪💻🧬
December 12, 2024 at 11:18 AM
📣 A new version of InterProScan (5.72-103.0) is available. You can download it here: ebi.ac.uk/interpro/abo... More info and documentation: interproscan-docs.readthedocs.io/en/latest/Re...
🧪💻🧬
🧪💻🧬
🚀 HUGE NEWS: Pfam 37.4 is LIVE!
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
June 20, 2025 at 8:47 AM
🚀 HUGE NEWS: Pfam 37.4 is LIVE!
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
4) Anvi'o databases containing KEGG/COG/PFAM/CAzyme annotations for all GlobDB genomes are avilable for download
June 10, 2025 at 11:22 AM
4) Anvi'o databases containing KEGG/COG/PFAM/CAzyme annotations for all GlobDB genomes are avilable for download
LNFF 🇲🇦 #D1F 🇲🇦
RS Berkane clinch second spot defeating SC Casablanca 2-1
RSB 2-1 SCC
Anissa Belkasmi 46
Oumaima Tayar 90+2
Itimi Mercy 🇳🇬 6
Results
RSB 2-1 SCC
HST 1-3 ITFF
WAC 6-1 CSST
AMLFF 4-3 RCAZ
PFAM 2-0 CRAH
SCCM 2-7 ARAFF
ASFAR 5-1 FUS
RS Berkane clinch second spot defeating SC Casablanca 2-1
RSB 2-1 SCC
Anissa Belkasmi 46
Oumaima Tayar 90+2
Itimi Mercy 🇳🇬 6
Results
RSB 2-1 SCC
HST 1-3 ITFF
WAC 6-1 CSST
AMLFF 4-3 RCAZ
PFAM 2-0 CRAH
SCCM 2-7 ARAFF
ASFAR 5-1 FUS
May 3, 2025 at 5:42 PM
LNFF 🇲🇦 #D1F 🇲🇦
RS Berkane clinch second spot defeating SC Casablanca 2-1
RSB 2-1 SCC
Anissa Belkasmi 46
Oumaima Tayar 90+2
Itimi Mercy 🇳🇬 6
Results
RSB 2-1 SCC
HST 1-3 ITFF
WAC 6-1 CSST
AMLFF 4-3 RCAZ
PFAM 2-0 CRAH
SCCM 2-7 ARAFF
ASFAR 5-1 FUS
RS Berkane clinch second spot defeating SC Casablanca 2-1
RSB 2-1 SCC
Anissa Belkasmi 46
Oumaima Tayar 90+2
Itimi Mercy 🇳🇬 6
Results
RSB 2-1 SCC
HST 1-3 ITFF
WAC 6-1 CSST
AMLFF 4-3 RCAZ
PFAM 2-0 CRAH
SCCM 2-7 ARAFF
ASFAR 5-1 FUS