How to use PSSM Profile Comparison Online

Compare protein profiles using probability overlap and a deliberate common background.

Upload two profile JSON files from PSSM Generation. Choose local or global alignment and inspect the aligned consensus sequences with original MSA/query coordinates.

How PSSM Profile Comparison Works

The position score is log2(sum(pA × pB / background)), a symmetric probability-overlap model rather than an HMM method. Both profiles must share a background unless you deliberately choose profile A, profile B, uniform, or custom frequencies as the common background. The comparison changes the scoring background without rebuilding either profile. The actual common frequencies are included in the download. Affine gaps use Gap Open + (k - 1) × Gap Extend bits. Smoothed profiles give finite scores; zero pseudocounts can leave impossible matches, and global alignment fails if no finite path exists. Scores have no calibrated E-values and are not PSI-BLAST equivalents.

Reading and downloading results

Upload the full-precision profile.json files from PSSM Generation as Profile A and Profile B. comparison.csv reports the total overlap alignment score, mode, chosen common background, inclusive retained-profile spans and gapped consensus strings. A Start/A End and B Start/B End index retained rows in their respective profiles, not original query residues.

alignment_positions.csv maps each display column to both profiles' retained positions, original MSA match columns and original query residues. CSV coordinates are one-based; blank means a gap or an unassigned query. The A/B residues are consensus residues and may differ from the source query. Overlap Score reports a residue-pair contribution before gap penalties; the total score includes those penalties. Empty local alignments have score zero and blank spans. Download common_background.csv for the full-precision normalized frequencies actually used in the comparison; changing the common background changes the comparison scores. The largest supported comparison has 1 million profile-by-profile positions. Hover headers or cells for detailed definitions.

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 Profile Comparison on Neurosnap

Using PSSM Profile Comparison 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 Profile Comparison on Neurosnap

To harness the capabilities of PSSM Profile Comparison, 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 Profile Comparison.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the PSSM Profile Comparison 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 Profile Comparison 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/

Similar Services

Explore related tools that support similar research workflows:

PSSM Generation

PSSM Sequence Alignment

PSSM Sequence Scan

ANARCI

Proudly supporting 50,000+ scientists worldwide, including 7,000+ leading biotech and global biopharma organizations.