skills.rest
pradyumnasagar
pradyumnasagarCOMMUNITY
Explore all skills by this author →
𝕏@pradyumnasagarGitHub

motif-search

Locate motifs and binding sites in DNA, RNA, and protein sequences using regex, IUPAC, PWMs, and JASPAR.

6|2|Updated Jun 11, 2026
Search Tags:#bioinformatics#sequence analysis#motif discovery#DNA/RNA motif search#PWM analysis
One-click install
npx skills add https://github.com/pradyumnasagar/open-research-skills --skill motif-search
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: motif-search
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/bioinformatics-sequence/motif-search
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill motif-search

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, regex, pyjaspar, numpy, motif, pyhmmer, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps researchers find motifs, patterns, and binding sites in sequences for analysis, by leveraging regex, IUPAC, PWMs, and modern motif databases like JASPAR.

Core Features & Use Cases

  • Pattern Detection: Locate known motifs, including transcription factor binding sites and protein recognition sites, using regex and IUPAC patterns.
  • PWM Analysis: Scan sequences with PWMs from motif databases for potential binding sites, adjusting for background sequences.
  • JASPAR Access: Retrieve motifs from JASPAR databases for advanced sequence analysis.
  • Use Case: Quickly identify a known transcription factor binding site in a promoter sequence using JASPAR PWMs.

Quick Start

Use the motif-search skill to identify known motifs in your sequence file 'sequence.fasta'.

Frequently Asked Questions about motif-search

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I identify transcription factor binding sites in DNA sequences using JASPAR PWMs?▼

You can locate known transcription factor binding sites and protein recognition sites by scanning your sequences with PWMs retrieved directly from the JASPAR database. This allows precise identification of regulatory elements while adjusting for background sequences.

What is the best way to search for DNA or RNA motifs using regex and IUPAC patterns?▼

You can search for DNA and RNA motifs by applying regex and IUPAC pattern matching to your sequences. This method locates known patterns and regulatory elements by defining flexible nucleotide codes for precise biological sequence analysis.

Can I use Biopython and pyjaspar to locate regulatory elements in a FASTA file?▼

Yes, you can locate regulatory elements in a FASTA file by leveraging Biopython for sequence parsing and pyjaspar for retrieving JASPAR motifs. This combination enables efficient scanning of sequences to identify potential binding sites.

Does this approach work with MEME and FIMO motif analysis tools?▼

Yes, this motif discovery approach is explicitly suitable for researchers working with motif analysis tools like MEME, FIMO, and JASPAR. It locates known patterns and binding sites, integrating smoothly into standard bioinformatics workflows.

Do I need specific bioinformatics dependencies to perform PWM analysis on my sequences?▼

Yes, performing PWM analysis requires installing specific bioinformatics dependencies including Biopython, regex, pyjaspar, numpy, and motif. These libraries provide the sequence parsing, database access, and mathematical frameworks necessary for motif discovery.

Related Skills

Explore More Education & Research Skills→
dralkhdralkh
74

biopython

Parse biological sequence, alignment, structure, BLAST, and Entrez data into Python workflows.

Community
Advanced
yf8578yf8578
1

jaspar-database

Access JASPAR to retrieve transcription factor binding profiles and scan DNA sequences.

Community
Intermediate
LeonChaoXLeonChaoX
783

glycoengineering

Scan protein sequences for N-glycosylation sequons and O-glycosylation hotspots.

Community
Intermediate
SciMate-AISciMate-AI
1

jaspar-database

Query transcription factor binding profiles from the JASPAR REST API.

Official
Intermediate