topufa

TOol for handling with Pdb-Uniprot-Fasta conversion and Alignment

Steps

1. In a given text file (.txt or .csv), searches for all PDB 4-digit codes

*in this version only searches for PDB codes using lowercase letters

*.pdf to be included

2. Fetch corresponding Uniprot IDs

3. Fetch corresponding FASTA

4. Create a BLAST database with these

5. BLASTp alignment between this database and your assigned input-query fasta file

6. Output several lists/csv files demonstrating the conversions generated throughout the script execution PLUS output_blastp.txt with the alignment results

Useful scenarios:

You want to automatically select several PDB codes mentioned in a text file and compare 'em with a given sequence of yours.

Place in folder:

• script1.py
• your query.fasta
• your text file (txt or csv)

References for installing/using standalone BLASTp:
https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata
https://www.ncbi.nlm.nih.gov/books/NBK52640/
https://krother.gitbooks.io/biopython-tutorial/content/BLAST.html