August 10, 2020
Using the UniFIRE image on HPC clusters with Singularity or with Podman
The latest UniFIRE Docker image of version 2020.5 can also be used with Singularity or Podman. This allows to use the UniFIRE image on platforms like HPC clusters where Docker is not available. The wrapper script docker/bin/run_unifire_docker.sh provides the new option "-s singularity" or respectively "-s podman" in order to simplify the usage of this new feature. For more information please refer to the README.
June 26, 2020
New ARBA rules in URML format available
With the latest update of our rules in URML format, the first release of rules generated by the Association-Rule-Based Annotator (ARBA) is available on FTP under ftp://ftp.ebi.ac.uk/pub/contrib/UniProt/UniFIRE/rules/arba-urml-latest.xml
ARBA rules are trained within a fully automated procedure on the manually annotated set of proteins UniProtKB/SwissProt. Protein coverage and annotation depth of ARBA is significantly improved compared to our legacy fully automated rule system SAAS. Because ARBA retains the major part of SAAS predictions, we discontinue to update SAAS rules. The last SAAS URML file of release 2020_03 will remain available on FTP under ftp://ftp.ebi.ac.uk/pub/contrib/UniProt/UniFIRE/rules/saas-urml-latest.xml
April 08, 2020
UniFIRE Docker image
We have added a Docker image to our container registry, which contains the UniFIRE software together with all its dependencies, including InterProScan. This image allows to run a generic UniFIRE workflow on a protein sequence input file in multi-FASTA format, without the need to install any software other than Docker. Please refer to the README for further information about how to use this new feature.
November 21, 2019
PIRsitePredict is integrated into UniFire
PIRsitePredict is a HMMER based system that predicates functional residues within uncharacterized proteins using position-specific site conditional template annotation rules (PIR Site Rules or PIRSRs) (PMC6389862). PIRSRs currently contains about 1250 rules.
July 12, 2019
New rules and template alignments
The latest UniRule and SAAS rules of version 2019_07 are available on FTP.
July 09, 2019
New mailing list for the UniFIRE project
We have created a mailing list where you can ask questions related to the UniFIRE project, get help to annotate your protein sequences, suggest new features, discuss your own contributions to the project, etc.
Also we will announce any changes or new features on this mailing list. Please fill in the subscription form, if you would like to subscribe to the mailing list.
July 09, 2019
Latest UniRule / SAAS rules and template alignments are available on FTP
We are pleased to announce that from now on we will regularly provide the latest UniRule and SAAS rules in URML format on FTP.
July 09, 2019
New public UniFIRE Gitlab Repository
UniFIRE source code is now available in this public Gitlab repository.
June 11, 2019
Code and rules in master branch have been updated
The most important new feature of the updated rules is the new format of Catalytic Activity predictions. Apart from the EC (Enzyme Classification) number and a text describing the activity, the new format contains references to the corresponding Rhea reaction ID (RHEA:16505). Furthermore it contains references to the molecules, which participate in the predicted reaction (e.g. RHEA-COMP:9845, CHEBI:29748). These identifiers allow to find information related to the predicted catalytic activity on Rhea and ChEBI website.