Visit http://mammoth.bcm.tmc.edu/uet. You can access pre-computed ET results of structures from the protein data bank, and even run traces on custom structures.
The PyETV plugin for the PyMOL molecular visualization platform can also access the pre-computed ET results and directly display them in PyMOL.
ET results are also available at http://mammoth.bcm.tmc.edu/ETserver.html.
We demonstrate how to use these tools with videos viewable from our YouTube channel.
If you know the UniProt ID or SwissProt accession number of your sequence, you may enter that ID into the ET Report Maker to get a human-readable document in PDF format, supplemented by the original data needed to reproduce the results quoted in the report
Alternatively, given the UniProt accession number or amino acid sequence in FASTA format, an Evolutionary Trace analysis request may be submitted through the web service: http://mammoth.bcm.tmc.edu/uet. The user will have the option whether to provide their own multiple sequence alignment and modify trace parameters through the service, or simply accept the default settings.
You can visit our YouTube channel for a demonstration and to learn more.
The query sequence must be included in the multiple sequence alignment. For example, if you provide a PDB structure, the sequence in the structure must match one of the sequences in the alignment. If you are using UET, the name of the query sequence can be specified in the Advanced Options section, near the upload box for the multiple sequence alignment file.
One can highlight multiple residues from the sequence window, just not by mouse-dragging and highlighting, which acts as a literal text highlighting on the HTML page.
To allow the user to explicitly specify and select a range of residue numbers, the sequence window includes boxes where starting and ending residue numbers can be entered. Clicking the adjacent button will toggle the selection of the range of residue numbers from start to end. The "Clear all" button clears the selections on both the sequence view and structure view (i.e. removes the spacefill display).
A mouse-click over a residue in the structure window will now select the corresponding one-letter code in the sequence window, as well as display the residue in spacefill mode.
The custom coordinates file in PDB format should contain only one chain, and if there are multiple chains in the file, the first chain is extracted and traced.
The pipeline for producing pre-computed trace analysis excludes chains shorter than 15 aa, which is one reason that not many pre-computed trace results can be found for short peptide chains. Short peptide chains do require special care to trace using non-default options, for example by changing the e-value threshold in the Advanced Options.
The two traces were computed using different trace parameters. The sequence identity thresholds used to select homologs from BLAST search results might have been different (i.e. the parameter values for "Restrict BLAST hits to minimum sequence identity:" and "Restrict BLAST hits to maximum sequence identity:" could have been different. In the pre-computed traces, they could have been 20% and 95%, while in the de novo traces, they could have been 28% and 98%). The databases could have been different as well. For example, one trace could have used "Custom NCBI", while the other used "Custom UniRef90". The parameter settings can be found in the "log" file included in the zip file of trace results.
The two traces were computed using different trace parameters. The sequence identity thresholds used to select homologs from BLAST search results might have been different (i.e. the parameter values for "Restrict BLAST hits to minimum sequence identity:" and "Restrict BLAST hits to maximum sequence identity:" could have been different. In the pre-computed traces, they could have been 20% and 95%, while in the de novo traces, they could have been 28% and 98%). The databases could have been different as well. For example, one trace could have used "Custom NCBI", while the other used "Custom UniRef90". The parameter settings can be found in the "log" file included in the zip file of trace results.
We are currently updating and retracing all chains in the database to use the same BLAST sequence database (e.g. UniRef90).
Once a week, the PDB files are updated through rsync and new PDB structures (those of type "prot" or "prot-nuc") are subject to evolutionary trace analysis. Once a month, the sequence databases are updated (Custom NCBI/NR, UniProt/Uniref). The total number of available trace results in the database and the time stamp are now displayed on the input page for PDB IDs.
Currently, Trace results for 139958 PDB chains are available. This information was last updated on Nov 19 18:33