How to use PSSM Sequence Scan Online

Find matching profile-length windows in longer proteins.

Upload a reusable profile and one or more longer protein sequences. Scan every ungapped window of the profile length, then report up to Top Windows per sequence above Minimum Score. Overlapping windows are allowed.

How PSSM Sequence Scan Works

Each window score is the sum of position-specific log-odds across the profile. No gaps or alignment penalties are used. Start and end coordinates in the CSV are one-based and inclusive. Sequences shorter than the profile appear in the summary with no windows; a score threshold may also leave a sequence without reported windows. Scores are most comparable across windows of the same profile. Scores are log-odds in bits, with no calibrated E-values or PSI-BLAST equivalence.

Reading and downloading results

Upload profile.json from PSSM Generation. windows.csv ranks reported windows across proteins by decreasing score and includes the protein name, inclusive start/end coordinates and window sequence. Rank 1 is the highest raw score; tied scores do not imply distinct biological support. Every window has the retained profile length.

summary.csv includes every submitted protein, even when no window is reported. Windows Scored is max(0, sequence length - profile length + 1). Passing Windows counts windows meeting Minimum Score before truncation; Reported Windows counts those retained after applying Top Windows to that protein. Scanned means scoring completed and does not guarantee a passing window. Sequence shorter than profile means no full-length window exists. Hover headers or cells for detailed definitions.

Submit up to 100 proteins, each up to 100,000 residues. Large profile/sequence combinations may need smaller jobs; the accepted limits are 2 million profile-by-sequence positions per protein, 5 million per batch and 100,000 reported windows per job. Scores compare windows of the same profile and background, not different profile models.

What is Neurosnap?

Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.

Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.

Advancing Discovery with PSSM Sequence Scan on Neurosnap

Using PSSM Sequence Scan on Neurosnap could drastically accelerate protein profile generation, inspection and candidate screening.

Reusable profiles: Retain full-precision probabilities and source coordinates.
Clear scoring: Interpret profile scores in bits.
Downloadable results: Inspect tables and alignment details.

How to Use PSSM Sequence Scan on Neurosnap

To harness the capabilities of PSSM Sequence Scan, researchers can follow this streamlined workflow within Neurosnap:

Access Neurosnap: Start by logging in to the Neurosnap website.
Select Tool: From the list of available tools, choose PSSM Sequence Scan.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the PSSM Sequence Scan job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.

Citations

Please cite the original work when using PSSM Sequence Scan in publications or research outputs.

Amani, Keaun, and Danial Gharaie Amirabadi. 2024. Neurosnap SDK Package. Software. https://github.com/NeurosnapInc/neurosnap.

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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