Select domain/s by name or PFAM/SMART accession as in CDD  
Domain query:

Select domain/s using sequences  

Enter a single protein sequence in either

    

  

Options
   Expect
   Filter
   Short or long report

About:
With this web-based tool you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.
Input:
You can either:
  • query using domain names or PFAM/SMART accessions. Multiple domain queries are separated by 'AND'.
  • or input a sequence or set of sequences containing the domains you are interested in.
  • Visual output:
    Domains are shown as bars, divided into colored areas proportional to the amount of domains of that type found in the eukaryotic proteomes included in the analysis (interpretation).
    Comparison of multiple domains:
    Multiple domains are compared based on their phylogenetic profiles and correlation of the phylogenetic distribution (interpretation).
    Applied datasets:
  • Proteomes: source databases
  • Domains: PFAM and SMART PSSMs from NCBI
  • Some data
     Domains which appear uniform distribution using chi-square tests and are present in at least 15 proteomes
     Domains which appear to be expanding in particular taxons using Dixon's outliers test (P value less than 0.05): plants exp, fungal exp, insect exp, chordata exp
    Domain query:
    With this form you can search in a dataset of around 4250 eukaryotic Pfam and Smart domains as included in the
    NCBI CDD database. A list of queries should be separated using ' AND '. Possible queries are domain names or domain accessions: 'sh3 AND sh2', 'SH3 AND SH2', 'PF00017 AND pfam00018'. A query for sh3 will match all domains containing SH3 as a substring: SH3, SH3BGR, SH3BP5
    Sequence query:
    With this form you can perform a rps-blast search with one or several sequences against the Pfam domains included in the
    NCBI CDD database. The phylogenetic distribution of all found domains is visualized and compared.
    Sequence query:
    With this form you can search in a dataset of around 4250 eukaryotic Pfam and Smart domains as included in the
    NCBI CDD database. A list of queries should be separated using ' AND '. Possible queries are domain names or domain accessions: 'sh3 AND sh2', 'SH3 AND SH2', 'PF00017 AND pfam00018'. A query for sh3 will match all domains containing SH3 as a substring: SH3, SH3BGR, SH3BP5
    Options:
    Expect:
    You can modify the E-value threshold applied on the rps-blast search of your sequence-set. False positive results are rare with the default setting of 0.01. Higher E-value tresholds give more false positives, while lower E-values increase reliability.
    Filter:
    You can determine whether a SEG low complexity filter should be applied to your sequence (T) or not (F). If filtering is turned off, false positive hits can increase in compisitionally biased regions.
    Short ot long report :
    The long report provides a separate listing of each domain that is coccurring with others in the set. The coccurrence of domains is a minumum requirement for their interaction.