Does this skill require a JASPAR API key?

No, the JASPAR REST API is open access and does not require an API key for standard queries and data retrieval.

Can this skill help with SNP impact analysis?

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

How do I search for a specific human transcription factor?

You can use the search functionality to filter by the TF name and the human taxonomy ID (9606) to retrieve relevant binding profiles.

What is the JASPAR database?

JASPAR is a gold-standard, open-access database containing curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs).

What matrix formats does the skill support?

The skill works with Position Frequency Matrices (PFMs) from JASPAR and can convert them into Position Weight Matrices (PWMs) for log-odds scoring.

JASPAR Database Tools

Name: JASPAR Database Tools
Author: henriquescastilho

byhenriquescastilho

•

Ciencia de Datos y ML

Queries the JASPAR database to analyze transcription factor binding sites and interpret regulatory genomic variants.

The JASPAR Database skill empowers Claude to interact with the premier open-access repository of transcription factor (TF) binding profiles. It provides comprehensive tools for bioinformaticians and researchers to search for position frequency matrices (PFMs), convert them into position weight matrices (PWMs), and perform sophisticated DNA sequence motif scanning. Whether you are investigating promoter regions, analyzing the impact of GWAS variants on gene regulation, or building gene regulatory networks, this skill streamlines the process of integrating JASPAR's high-quality, non-redundant experimental data directly into your computational biology workflows.

Características Principales

01Perform DNA sequence scanning for potential binding sites with configurable scoring thresholds.

02Evaluate the regulatory impact of SNPs and variants on motif binding affinity.

03Access over 1,200 curated, non-redundant TF binding profiles from the JASPAR 2024 CORE collection.

041 GitHub stars

05Generate position weight matrices (PWMs) for log-odds scoring of genomic sequences.

06Search profiles by TF name, taxonomy ID, species, family, or structural class.

Casos de Uso

01Predicting transcription factor binding sites within specific promoter or enhancer sequences.

02Analyzing motif enrichment in ChIP-seq or ATAC-seq peak data for gene regulation studies.

03Interpreting the functional impact of GWAS/eQTL variants on regulatory motifs.

Características Principales

01Perform DNA sequence scanning for potential binding sites with configurable scoring thresholds.

02Evaluate the regulatory impact of SNPs and variants on motif binding affinity.

03Access over 1,200 curated, non-redundant TF binding profiles from the JASPAR 2024 CORE collection.

041 GitHub stars

05Generate position weight matrices (PWMs) for log-odds scoring of genomic sequences.

06Search profiles by TF name, taxonomy ID, species, family, or structural class.

Casos de Uso

01Predicting transcription factor binding sites within specific promoter or enhancer sequences.

02Analyzing motif enrichment in ChIP-seq or ATAC-seq peak data for gene regulation studies.

03Interpreting the functional impact of GWAS/eQTL variants on regulatory motifs.