PANDIT+

KeywordPfamClanGene   

 Download PANDITplus

The entire PANDITplus database is available for download. In publication of research that makes use of the data, a citation should be given of:

  • Dimitrieva S. and M. Anisimova. 2010. PANDITplus: Towards better integration of evolutionary view on molecular sequences with complementary bioinformatics resources. Trends in Evol Biol.

If you use the additional information about intrinsically disordered regions please cite:

  • Szalkowski AM, Anisimova M, 2011 Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions. PLoS ONE 6(5): e20488. doi:10.1371/journal.pone.0020488

 Create your own PANDITplus

You can create your own instance of a PANDITplus database by building one de novo. To build the PANDITplus database from scratch, you will need a MySQL server and the PANDITplus database SQL source. Installation packages and documentation on the MySQL database itself can be found on the MySQL website. The PANDITplus SQL source can be found here:

panditplus_v_1_1_031209.sql.gz

 Local installation from database dumps

PANDITplus database can be downloaded as a MySQL database dump and reconstituted on any system where MySQL is running. The data is also available as SQL statements for use with other database management systems. The ER diagram of PANDITplus is shown here.

Families family.sql.gz
family.txt.gz
fam_literature_references.sql.gz
fam_literature_references.txt.gz
literature_references.sql.gz
literature_references.txt.gz
family_seq.sql.gz
family_seq.txt.gz
interactions.sql.gz
interactions.txt.gz
family_pdb.sql.gz
family_pdb.txt.gz
taxonomy.sql.gz
taxonomy.txt.gz
version.sql.gz
version.txt.gz
Clans clans.sql.gz
clans.txt.gz
family_clans.sql.gz
family_clans.txt.gz
clan_lit_refs.sql.gz
clan_lit_refs.txt.gz
Estimates from Markov codon substitution models model0.sql.gz
model0.txt.gz
model1.sql.gz
model1.txt.gz
model2.sql.gz
model2.txt.gz
model7.sql.gz
model7.txt.gz
model8.sql.gz
model8.txt.gz
modelhyphy.sql.gz
modelhyphy.txt.gz
sites_positsel.sql.gz
sites_positsel.txt.gz
Gene Ontologies family_go.sql.gz
family_go.txt.gz
go_term.sql.gz
go_term.txt.gz
KEGG Pathways family_kegg_pathway.sql.gz
family_kegg_pathway.txt.gz
kegg_pathway.sql.gz
kegg_pathway.txt.gz
kegg_pathway_hierarchy.sql.gz
kegg_pathway_hierarchy.txt.gz
kegg_genes.sql.gz
kegg_genes.txt.gz
kegg_ncbientrez_map.sql.gz
kegg_ncbientrez_map.txt.gz
kegg_pfam_map.sql.gz
kegg_pfam_map.txt.gz
Intrinsically disordered regions fam_disorder.sql.gz
fam_disorder.txt.gz
disorder_regions.sql.gz
disorder_regions.txt.gz
Bgee expression data fam_bgee_expression.sql.gz
fam_bgee_expression.txt.gz
bgee_anatomical_struct.sql.gz
bgee_anatomical_struct.txt.gz
bgee_stages.sql.gz
bgee_stages.txt.gz
bgee_hierarchy.sql.gz
bgee_hierarchy.txt.gz
bgee_anatomical_struct_relations.sql.gz
bgee_anatomical_struct_relations.txt.gz
bgee_genes.sql.gz
bgee_genes.txt.gz
Human Proteinpedia expression data hupa_hprd_tissue_expression.sql.gz
hupa_hprd_tissue_expression.txt.gz
hupa_hprd_disease_tissue_expression.sql.gz
hupa_hprd_disease_tissue_expression.txt.gz
kegg_hprd_map.sql.gz
kegg_hprd_map.txt.gz
Human disease association disease_gene.sql.gz
disease_gene.txt.gz
disease_association.sql.gz
disease_association.txt.gz
OMIM links kegg_omim_map.sql.gz
kegg_omim_map.txt.gz

 Bulk download of alignments and trees

Amino acid (AA) and nucleotide (DNA) sequence alignments for all families from PANDIT (each family AA and DNA alignment/tree represented in separate file) can be downloaded from here:

Alignments AA_alignments.tar.gz
DNA_alignments.tar.gz
Trees without branch lengths AA_treesNoLengths.tar.gz
DNA_treesNoLengths.tar.gz
Trees with branch lengths AA_treesWithLengths.tar.gz
DNA_treesWithLengths.tar.gz

Complete AA and DNA sequence alignments together with phylogenies and associated information can be obtained also from PANDIT