A standalone software tool that retrieves subcellular location, topology annotation, signal peptides, regions and amino acid modifications from UniProt database. The output is a compressed (.gz) ready-to-use file in the Perseus software platform
The software requires only a standard computer with enough RAM to support the operations defined by a user. Windows is the only supported OS at the moment. The latest release of the software (version 1.0.4) has been tested on Windows 10 operating systems with minimum 8GB of RAM and a dual-core i5-4200M CPU @2.50GHz. For optimal performance, we recommend a computer with the following specs:
RAM: 16+ GB CPU: 4+ cores, 3.0+ GHz/core
and internet connection of speed > 25 Mbps.
No installation is required to run the software. A compiled version is provided under the Releases section. UniProt Annotation Retriever requires Microsoft .NET Framework 4.5 (https://www.microsoft.com/en-US/download/details.aspx?id=30653) to be installed on your PC.
You can simply download and run the compiled UniProt Annotation Downloader.exe executable file which is located under the Releases section of this GitHub repository. Additionally, a sample file with a list of UniProt IDs is provided under the test_files directory for testing purposes. Press the button 'Select File', choose a file which contains a list of UniProt IDs, select or deselect the annotation categories of your interest (by default all options are selected and will be downloaded) and click 'Start'. The tool retrieves in real-time all the selected features for the given protein IDs from UniProt.
Next, locate the proteinAnnotations.txt.gz file which will be created by the software and simply copy and paste it (you can optionally rename it as well) into the bin/conf/annotations folder of the Perseus software. Re-start Perseus (in case it's already open) and you will be able to see the new annotation in Perseus GUI by selecting Annot. columns --> Add Annotation , as shown below.
For questions, suggestions, bug-reports or feedback, please get in touch by email:
- gkoulouras {at} gmail {dot} com
If you use this tool or data derived from this software in your research work please consider citing the following DOI: 10.5281/zenodo.6645639
This project is licensed under the Apache 2.0 license, quoted below.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.