Uniclust Webserver User Guide

The server can perform a full-text search for keywords and sequence identifiers of over a hundred biological databases linked to UniProt entries. Searches will give a list of clusters as result, each linking to a cluster page. The user can chose the Uniclust version.

Multiple Sequence Alignment

Interactive BioJS alignment viewer. The alignment can be navigated by scrolling or clicking inside the overview box. By using the export buttons either a selection or the whole MSA can be downloaded.

The first sequence always shows the cluster consensus sequence. Above the MSA a sequence logo can be seen.

Our domain annotations are shown as colored bars on top. There are annotations available for Pfam, SCOP and PDB. The domain annotations can be hidden.

Annotations

Name Query Position Target Position E-value

PDB

1tf6_A 204-411 10-188 1.46e-31
2eln_A 409-442 2-36 2.86e-05
2ab3_A 174-192 3-22 7.75001e-05

PFAM

PF06524.9 172-442 38-265 1.35e-35

SCOP

d2csha1 354-410 1-53 7.34e-18
d2csha1 234-288 1-53 9.24e-17
d1sp2a_ 205-234 1-31 3.3e-12
d1zfda_ 293-321 1-30 3.4e-11
d1ubdc4 326-351 2-28 6.00027e-11
d2glia5 415-442 1-29 1.06e-07
d1bhia_ 171-198 4-32 0.000449
d2dlqa4 455-476 4-26 0.00142

Shows a list of our domain annotations, also idicated as the colored domain annotation bars in the MSA viewer. The target name, query position, target position and E-value columns are shown. Clicking a target name navigates to the respective external resource, while clicking the query position navigates the MSA viewer directly to the position of the domain annotation. The lists are sorted by E-value.

Phylogram

An expandable taxonomic tree of the species represented in the cluster. Leaf nodes are shown in green, these are the species that are shown in the MSA. Intermediate nodes are shown in orange, the first level of the itermediate node tree is shown by default. The labels of all other levels can be shown by hovering over nodes. Upon clicking a node, all children leaf nodes will be selected in the MSA. If there are multiple proteins of one species the number will be shown on the leaf nodes.

The tree in its expanded form shows all labels. The labels and nodes can also be clicked to select the subtree in the MSA viewer.

Keywords

Summary of all UniProt Keywords over all cluster members, shown on log scale. Colors aid with visual identifications.

Evidence

Summary of all UniProt evidence values of all cluster members, shown on log scale. Colors aid with visual identifications. Five different levels are annotated:

  • Experimental evidence at protein level
  • Experimental evidence at transcript level
  • Protein inferred from homology
  • Protein predicted
  • Protein uncertain

Downloads & Schedule

A description of the downloads is also available.

We will update the Uniclust databases every two months following the new UniProt release. To keep the cluster identifiers stable between updates, we do not recluster from scratch but instead update the clustering incrementally, add the new sequences to existing clusters, creating new clusters, and removing deprecated sequences. To avoid excessive computational demands, we recompute the MSAs and sequence annotations only during the reclustering step once per year and for major UniProt releases.