needle tools file formats

BMERC : Index of needle software : needle tools : File formats

With a few exceptions (such as some extra documentation on the format of Protein Data Bank ATOM records), these file formats have been developed mostly at BMERC. They are subject to revision without notice.

For more information, please see the needle tools home page.

Table of contents

• needle tools file formats
  • File formats related to protein sequence
    • IG sequence format
    • Table (.tbl) file format
    • FA sequence format
    • BLAST database format
    • BLAST summary file format
  • File formats relating to structure
    • Segment file format
    • Abbreviated DSSP file format
    • .nexp (exposure) file format
    • Core file format
    • Internal "ss" format
    • Internal "core abstraction" file format
  • Alignment file formats
    • FSSP alignment format
    • ctimap format
    • Homolog file format
  • MRF score and environment formats
    • Environment file format
    • Counts file format
    • Score file format
  • Dependency file formats
    • Core definition file format
      • Core naming convention
      • Core chain specification syntax
      • Core definition file example
      • Naming of other files
      • Old prefix naming convention
    • Cross-validation set file format
  • VVenv file formats
    • Hyperenv file format
    • VVenv singleton file format
  • Notes on PDB ATOM record format
    • ATOM record format
    • Notes on atom serial numbers
    • Notes on atom naming
    • Notes on atom variants
    • Notes on amino acid abbreviations
    • Notes on chains
    • Notes on sequence number and insertion code
    • Notes on atom occupancies