Hi guys,
I need to present a family of proteins in a paper. Could anyone suggest a contemporary c graphic representation of protein family? Perhaps, you saw good examples of that in literature? Information I think to to include in the introductory figure: sequence alignment with consensus sequence, phylogenetic tree, post-translational modifications, secondary structure prediction and repeats. What else you would expect to see in a good figure and supporting text?
I would also appreciate if you could suggest your favourite bioinformatic tools for the listed protein analysis tasks.
Many thanks,
Oleksiy
A neat way of presenting families that has come up in the last few years - especially from the Babbitt group at UCSF - are 'sequence similarity networks'. Search for it and read the respective papers' methods sections. In a nutshell: All you need is a free network visualisation tool like Cytoscape, then you do an all-v-all similarity search of the proteins in your family (or just representative ones if the network gets too big/'crowded', e.g. by using the cluster representative of a sequence clustering tool like CD-HIT, e.g. clustering at 60% sequence identity) using BLAST, to get a list of protein pairs and their similarity (you could use -log(E-value) or the seq. id. value). Give this to Cytoscape. Then use, e.g., organic layout. In addition, colour the network by protein function, e.g., using EC numbers (you would give each full 4-level EC i.e. specific enzyme function in your family a corresponding colour), or using GO or KEGG, if you have non-enzymatic sequences in your family. That all is one way of doing it, roughly. The papers will tell you more.
HTH,
Rob
Sequence logo or cartoon 3-D structure colored by conservation is also a possibility.
Hi, I also advice Clans (http://bioinfoserver.rsbs.anu.edu.au/programs/clans/) as a short version of Robert's suggestion. To each clan you can add a domain architecture, EC functions etc. Good luck :)
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