What genomic data can I access with the JASPAR skill?

You can access over 1,210 non-redundant transcription factor binding profiles for 164 eukaryotic species, including humans, from the JASPAR CORE and UNVALIDATED collections.

Does it require external bioinformatic tools?

The skill provides Python-based implementations for matrix conversion and sequence scanning, though it can also be used in conjunction with libraries like Biopython or tools like FIMO.

Can this skill predict the impact of genetic mutations?

Yes, it includes specialized workflows to compare reference and alternative sequences to determine if a variant disrupts an existing motif or creates a new binding site.

How do I search for specific species in JASPAR?

You can search using common names or NCBI taxonomy IDs (e.g., '9606' for Homo sapiens) via the provided API search functions.

JASPAR Database Genomics

Name: JASPAR Database Genomics
Author: Yezez9

byYezez9

0•

데이터 과학 및 ML

Access and analyze transcription factor binding profiles from the JASPAR database to predict binding sites and interpret regulatory variants.

The JASPAR Database skill empowers researchers and developers to integrate the gold-standard JASPAR 2024 database directly into their genomic workflows. It provides specialized capabilities for retrieving curated transcription factor (TF) binding profiles, converting position frequency matrices (PFMs) into weight matrices (PWMs), and performing sophisticated sequence scanning. Whether you are interpreting GWAS variants, analyzing promoter regions, or constructing gene regulatory networks, this skill streamlines the process of linking TFs to their target DNA sequences through standardized API interactions and validated implementation patterns.

주요 기능

01Automated conversion of PFMs to PWMs with custom pseudocount adjustment

02Comprehensive search by TF name, species taxonomy ID, class, or family

03REST API integration for real-time JASPAR 2024 database queries

040 GitHub stars

05High-performance DNA sequence scanning across both forward and reverse strands

06Variant impact assessment for predicting regulatory motif disruption or gain

사용 사례

01Interpreting the impact of SNPs and eQTL variants on regulatory elements

02Identifying enriched TF motifs within ChIP-seq or ATAC-seq peak data

03Predicting transcription factor binding sites in promoter and enhancer regions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent jaspar-database

For use in Claude.ai and ChatGPT

주요 기능

01Automated conversion of PFMs to PWMs with custom pseudocount adjustment

02Comprehensive search by TF name, species taxonomy ID, class, or family

03REST API integration for real-time JASPAR 2024 database queries

040 GitHub stars

05High-performance DNA sequence scanning across both forward and reverse strands

06Variant impact assessment for predicting regulatory motif disruption or gain

사용 사례

01Interpreting the impact of SNPs and eQTL variants on regulatory elements

02Identifying enriched TF motifs within ChIP-seq or ATAC-seq peak data

03Predicting transcription factor binding sites in promoter and enhancer regions