PSSMSearch is a web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites. PSSMSearch analyses proteomes for regions with significant similarity to a specificity determinant model built from a set of aligned functional peptides. Query peptides can be provided by the users or retrieved from the ELM database. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the specificity determinant model and users can modify the model to add prior knowledge of specificity determinants through an interactive PSSM heatmap.
If you use PSSMSearch for your research, please cite the most recent publication:
- Norman Davey and Izabella Krystkowiak: Science Foundation Ireland Starting Investigator Research Grant
- Jean Manguy: Enterprise Ireland grant to Food for Health Ireland
PSSMSearch is available for download and use under a GNU General Public License. It allows the users (individuals,
organizations, companies) to run, study, share (copy), and modify the software. However, it requires that when
distributing derived works, the source code of the work must be made available under the same license.
For the full license please see GNU GPL v3 licence.
- The developers of PSSMSearch require attribution for its service.
- Any use of the PSSMSearch is non-confidential.
- Users of PSSMSearch agree not to attempt to use any part of the UCD computers, files or networks apart from
through the service interfaces provided.
- The developers of PSSMSearch do not guarantee the accuracy of any data contained herein, nor the suitability of
the PSSMSearch web service for any purpose.
- If any single user exploits the PSSMSearch web service to a level that prevents, or looks set to prevent, the
developers of PSSMSearch providing services to others, the developers of PSSMSearch may discontinue service to
that user. The developers of PSSMSearch will then contact the user to discuss their needs and how (and if) these
can be met.
- For planning and scientific review purposes, the developers of PSSMSearch will keep records of usage. Logs of
usage may also be maintained for the purposes of monitoring and improving services, and measuring the impact a
particular service has on our resources.
- The developers of PSSMSearch will make reasonable effort to maintain continuity of service and provide adequate
warning of any changes or discontinuities. However, the developers of PSSMSearch accepts no responsibility for the
consequences of any temporary or permanent discontinuity in service.
- The developers of PSSMSearch itself places no restrictions on the use or redistribution of the data available
via the PSSMSearch service. However, the original data may be subject to patent, copyright, or other intellectual
property rights claimed by third parties. It is the responsibility of users of the service to ensure that their
exploitation of the data does not infringe the rights of such third parties. The developers of PSSMSearch can
neither comment on the validity of their claims nor grant unrestricted permission regarding the use of the data.
- Any feedback on the service is welcome.
- The developers of PSSMSearch are not liable to you or third parties claiming through you, for any loss or
- The developers of PSSMSearch reserves the right to alter these terms at any time in order to ensure their
appropriateness to the PSSMSearch mission.
This web service uses the following libraries and resources:
- Colors from www.ColorBrewer.org by Cynthia A. Brewer, Geography, Pennsylvania State University.
- pandas 0.15.1 BSD
- SQLAlchemy 0.9.8 MIT License
- alembic 0.6.7 MIT
- futures 2.2.0 BSD
- pyramid 1.5.2 BSD-derived (http://www.repoze.org/LICENSE.txt)
- cornice 0.17 MPLv2.0
- waitress 0.8.9 ZPL 2.1
- colander 1.0 BSD-derived (http://www.repoze.org/LICENSE.txt)
- WebTest 2.0.18 MIT
- requests 2.6.0 Apache 2.0
- psycopg2 2.5.4 LGPL with exceptions or ZPL
- numpy 1.9.1 BSD
- biopython 1.64 Biopython License Agreement or BSD
- scipy 0.13.0b1 BSD
- pyramid-exclog 0.8 BSD-derived (http://www.repoze.org/LICENSE.txt)
- EmberJS MIT
- Bootstrap MIT
- Grunt MIT
- Font Awesome MIT
- Jquery MIT
- FileSaver MIT
- StickyTableHeaders MIT
- Sentry BSD
- pq MIT
- autoprefixer MIT
- babel-plugin-lodash MIT
- babel-plugin-react-css-modules BSD-3-Clause
- babel-plugin-transform-react-remove-prop-types MIT
- babel-preset-env MIT
- babel-runtime MIT
- classnames MIT
- cookies-eu-banner MIT
- css-loader MIT
- d3-scale BSD-3-Clause
- deep-equal MIT
- expose-loader MIT
- fast-memoize MIT
- flexbox-react MIT
- history MIT
- html-webpack-plugin MIT
- immutability-helper MIT
- lodash-es MIT
- lodash MIT
- node-sass MIT
- pluralize MIT
- postcss MIT
- promise-polyfill MIT
- prop-types MIT
- react-copy-to-clipboard MIT
- react-dom MIT
- react-helmet MIT
- react-hot-loader MIT
- react-redux MIT
- react MIT
- redux-act Apache-2.0
- redux-batched-actions MIT
- redux-logger MIT
- redux-thunk MIT
- redux MIT
- sass-loader MIT
- save-svg-as-png MIT
- semantic-ui-css MIT
- semantic-ui-react MIT
- webpack MIT
- whatwg-fetch MIT
We are using Google Analytics to gather statistics about the uses of PSSMSearch.
The role of this cookie is to count the users and to distinguish the new users from
the returning users. Expiration: 2 years.
The role of this cookie is to survey the frequency of requests. Expiration: 10
More information about Google Analytics cookies can be found here.
Contact information are available here.
You can also report issues on Bitbucket: