Convert NCB to NDB

Understanding ncb and ndb file formats

NCB files are NCBI BLAST database files used by the National Center for Biotechnology Information's BLAST (Basic Local Alignment Search Tool) suite. These files store nucleotide or protein sequence databases in a binary format optimized for fast searching and alignment.

NDB files, on the other hand, are Nucleic Acid Database files, which store three-dimensional structural data of nucleic acids. The NDB format is used primarily for archiving and sharing structural information about DNA and RNA molecules.

Can you convert ncb to ndb?

Direct conversion from NCB to NDB is generally not possible because these formats serve fundamentally different purposes: NCB files contain sequence data for searching, while NDB files contain 3D structural data. There is no automated tool that can directly convert an NCB BLAST database into an NDB structure file.

Alternative approaches

If you need to obtain an NDB file for a sequence in an NCB database, you must:

1. Extract the sequence from the NCB database using BLAST or blastdbcmd.
2. Search for the corresponding 3D structure in the Nucleic Acid Database (NDB) or Protein Data Bank (PDB).
3. Download the NDB file if available.

This process is manual and depends on whether a structure exists for your sequence of interest.

Recommended software and tools

• NCBI BLAST+ Suite: Use blastdbcmd to extract sequences from NCB files.
• NDB/PDB Web Portals: Search for and download NDB files for known structures.

There is no direct converter between NCB and NDB formats due to their different data types and purposes.

Summary

While both NCB and NDB files are important in bioinformatics, they are not interchangeable. To move from sequence data (NCB) to structural data (NDB), you must extract the sequence and search for its structure in public databases. No software currently automates this conversion.