jaspar

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

rbioapi: User-Friendly R Interface to Biologic Web Services' API

Motif discovery for DNA sequences using multiobjective optimization and genetic programming.

Pipeline: Identification of cis-regulatory elements by matrix scoring and analysis of supporting empirical biological data.

Pipeline: Identification of cis-regulatory elements by matrix scoring and conservation.

race a noncoding disease variant to the transcription-factor motif it disrupts — from DNA sequence — using ChromBPNet, in-silico mutagenesis, and JASPAR. Built with Claude Science for the Life Sciences hackathon.

RESTful web service for storing and managing JASPAR TF motifs' information

A browser workbench for DNA, RNA and protein sequence patterns: 523 documented motifs, live database retrieval, and a chance-corrected verdict on every match. Patterns are s-expressions; the page has no server and no dependencies. Also with an AI assistant generating s-expressions from natural language descriptions.

Computational biology toolkit and agent skill for JASPAR transcription factor binding profile visualization, sequence logo rendering, PFM/PPM/PWM matrix analysis, dual-strand DNA sequence scanning, and interactive HTML5 dashboards.

Reproducible Neo4j knowledge graph integrating Arabidopsis DAP-seq, motifs, gene annotation, and Y2H evidence.