Introduction
Background
Multi-domain proteins have evolved by insertions or deletions of distinct protein domains. Tracing the history of a certain domain combination can be important for functional annotation of multi-domain proteins, and for understanding the function of individual domains. In order to analyse the evolutionary history of the domains in multi-domain proteins it is desirable to inspect a phylogenetic tree based on sequence divergence together with the modular architecture of the sequences superimposed on the tree.
How to use it
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The first step to create the tree is, to enter a valid PFAM-family identifire (Name or ID).
If the red symbol appears, it means that the identifier is not right or doesn’t exist. The green symbol means that the PFAM-family has been found.
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The next step is to choose the type of query you want.
The standard query will calcuate the distances of a specific number of alignments to the one you enter in the next step and display a tree after it is finished.
The flexible one requires a neighbourhood chosen by the user. All the alignments should be in the previous chosen PFAM-family.
for the standard query
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Choose the type of dataset.
If you take full, it can take a few minutes to get all required Data from PFAM. Also there might be families which don’t support the full dataset, since they are too large.
If you take the NCBI dataset, please keep in mind, that the identifier might be different!
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Next you enter the sequence identifier.
- Last but not least enter the number of neighbours you want around the previous entered sequence (0-300).
for the flexible query
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Enter a list of sequence-identifiers from which the tree should be build.
(Those sequences have to be in the same PFAM-Family)
Please separate the sequence identifiers with line breaks.
Do not separate with any characters like in this example with “;”!
Do not use spaces as separator!