Query JASPAR for transcription factor binding site profiles and matrices.
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-jaspar
Please help me install this Agent Skill. Skill: db-jaspar Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-jaspar Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-jaspar
This Skill helps researchers and bioinformaticians quickly access and utilize the JASPAR database to understand transcription factor binding sites, aiding in the interpretation of genomic regulatory elements and variants.
Use the db-jaspar skill to search for transcription factor profiles for the human species.
High-intent search queries and answers about installing and using this skill.
To retrieve transcription factor binding profiles from the JASPAR database, you can search by TF name, species, or class to fetch specific Position Frequency Matrices (PFMs) and convert them to Position Weight Matrices (PWMs) for regulatory genomics analysis.
Yes, you can scan a given DNA sequence for transcription factor binding sites using PWMs. This process predicts potential binding locations within your sequence to help interpret genomic regulatory elements.
To analyze the impact of genetic variants on transcription factor binding sites, you can use this functionality to assess how sequence changes might affect TF binding affinity and disrupt regulatory elements within the genome.
In motif analysis, a PFM (Position Frequency Matrix) represents the observed nucleotide counts at each position, while a PWM (Position Weight Matrix) converts these frequencies into log-odds scores to evaluate sequence binding affinity.
Yes, you need numpy installed to query JASPAR matrices for motif analysis. The skill requires both the requests and numpy dependencies to fetch profiles from the database and perform the necessary numerical calculations.
Yes, you can search for transcription factor profiles by species and class. This allows you to filter JASPAR database queries to find specific TF binding site profiles relevant to your target organism or protein classification.
felixboehmQuery JASPAR transcription factor binding profiles and scan DNA sequences via REST API.
AlterLab-IEURetrieve JASPAR transcription factor binding profiles and scan DNA sequences for motif sites.
pradyumnasagarLocate motifs and binding sites in DNA, RNA, and protein sequences using regex, IUPAC, PWMs, and JASPAR.
Yezez9Query JASPAR transcription factor binding profiles via REST API and Python.
