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The Genomic Threading Database

Liam J. McGuffin & David T. Jones

The Genomic Threading Database (GTD) was a database of structural assignments to the proteins of whole proteomes formerly funded by the BBSRC. GenTHREADER was used to perform fold assignments for 261 complete genomes. Interested users can now find equivalent data and functionality via Gene3D.


Gene3D is a CATH project which assigns structural domains and and domain architectures to whole proteomes. It uses a variety of technologies including SiMAP, HMMER, SAM and GenTHREADER. You can scan your own sequences for domains using their Sequence Scan service or search the database with BLAST


Users who still need to cite the GTD should cite the following references:

The GTD

  • McGuffin, L. J., Bryson, K., Street, S. A., Sorensen, S. A. & Jones, D. T. (2004) The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res., 32, D196-D199.
  • McGuffin, L. J., Street, S. A., Sorensen, S. A. & Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20, 131-132.


GenTHREADER

  • McGuffin, L. J., Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
  • Jones, D. T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287: 797-815.