How to Convert a PDB to a FASTA

DNA can be be analyzed much more simply with the FASTA format.

The PDB file extension stands for "protein data bank" and contains within it text describing the three-dimensional structure of molecular proteins. It is used to store information in the protein data bank, which is an ever-growing database that organizes all of the known proteins. The FASTA file type is used by DNA analysis software to make two-dimensional representations of the proteins and assess their similarity. PDB files can be converted into FASTA files, so that these two-dimensional representations of proteins can be studied. The two-dimensional representations are far simpler to analyze and compare than the three-dimensional version, and it is for this reason that researchers sometimes prefer to do their work in FASTA software.

Things You'll Need

• Computer with Windows XP, VISTA or 7

Instructions

1. Download the Advanced Protein Sequence Converter linked in Resources. This is the only available software that will convert PDB to FASTA.

2. Install the Advanced Protein Sequence Converter onto your computer.

3. Open the advanced Protein Sequence Converter program.

4. Click "File" and then "Open File."

5. Select your PDB file from the browser window that opens.

6. Click "Open."

7. Choose "To FASTA Format" in the "Export" heading on the lower right side of the program.

8. Click "Options" and then "Settings."

9. Choose the string length you would prefer your FASTA file to be exported into.

10. Click "OK."

11. Click the "Export" button. Your PDB file will now be converted into a FASTA file with the protein string lengths that you designated.

References

• Fileinfo: .pdb file extension
• Fileinfo: FASTA file extension

Resources

• Softpedia: Advanced Protein Sequence Converter