PANDIT: Protein and Associated Nucleotide Domains with Inferred Trees

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What happened to PANDIT and the PANDIT website?

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.  Efforts to obtain renewed funding after 2008 were unfortunately not successful.  PANDIT has therefore been frozen since November 2008, and its data are not updated since September 2005 when version 17.0 was released (corresponding to Pfam 17.0).  The existing data and website remain available from these pages, and should remain stable and, we hope, useful.

PANDITplus

Users of PANDIT may also be interested in the PANDITplus database, an extension of PANDIT which integrates data from a variety of reliable and curated bioinformatics sources including pre-computed estimates from evolutionary codon models, data on protein interactions, functional and chemical pathway annotation, gene expression, and association with disease. PANDITplus is found at this link.

 

PANDIT description

PANDIT Version 17.0, September 2005, 7738 families

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains:

  • the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0)
  • nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as ‘templates’
  • protein sequence alignments restricted to the family members for which nucleotide sequences are available
  • inferred phylogenetic trees for each alignment

The latest Pandit paper was published in NAR (2006): click here to download it!

Pandit version 17.0 is now online! From version 17.0, Pandit now includes an assessment of alignment quality based on HMM methodology. Phylogenies in Pandit are built ignoring alignment regions that are deemed unreliable. See the release notes for further details.

The 'Pandit' database name has been cited as "remarkably creative" and "apt" (Galperin 2005:D5 [Nucl. Acids Res. 33:D5-D24]).

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Interactive WWW access to PANDIT

 

Download access to PANDIT

Download the PANDIT database:

 

Copyright notice for PANDIT

The full text of the GNU Library General Public License under which PANDIT is licensed