GeneSeq

A CRISPR gRNA mapping tool that:

• Gene & Transcript Retrieval via Ensembl

  • Fetches gene metadata, transcript lists, and cDNA sequences using the Ensembl REST API.

• Customizable PAM Pattern & Target Length

  • Supports user-defined PAM sequences (e.g., NGG, NNGRRT) and target site lengths (e.g., 15–25 bp).

• Strand-Aware Target Detection

  • Scans both sense and antisense strands for target sites matching criteria.

• Raw Sequence Caching

  • Stores fetched sequences as .txt files in /datalibrary/rawsequences to avoid repeated API calls.

• Variant Overlap Reporting

  • Displays the number of variants overlapping the selected gene from Ensembl variation data.

• Auto-Named SQLite Target Databases

  • Stores results in uniquely named .db files based on transcript ID, PAM, and target length.

• Smart Database Reuse

  • Checks if the same parameter combination has already been processed — skips redundant computation.

How to Use

1. Run grna_map.py
2. Enter a gene, The PAM sequence and the target length desired.
3. If the combination of parameters specified above already has a database, access it from datalibrary/sqlite_dbs
4. If not, a new DB will be created as db_{ENSEMBL_TRANSCRIPT_ID}_{PAM}_{TARGET_LEN}_.db after scanning for matches.

Folder Structure

GeneSeq/
|--- datalibrary/
|------|--- rawsequences
|------|--- sqlite_dbs
|--- db_access/
|--- ensembl_fetch/
|--- raw_seq_access/
|--- seq_scan/
|--- grna_map.py
|--- README.md

Folder and File Purposes

rawsequences -> repository with gene sequences locally as {GENE SYMBOL}_{ENSEMBL_TRANSCRIPT_ID}_seq.txt files.
sqlite_dbs -> unique sqlite dbs for each variation of params - db_{ENSEMBL_TRANSCRIPT_ID}_{PAM}_{TARGET_LEN}_.db
db_access -> to check if a db exists, if not - functions to create and access it.
ensembl_fetch -> fetching various genetic data from ensembl
raw_seq_access -> functions to directly access to the local datalibrary/rawsequences bypassing the DB.
seq_scan -> scans the gene sequence for matches based on GENE, PAM and TARGET LENGTH.
grna_map -> main function