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bioRxiv · 10.1101/2024.10.30.621149

Sequence clustering with PaSiMap in Jalview

Morell, T.·Procter, J.·Barton, G. J.·Diederichs, K.·Mayans, O.·Fleming, J. R.
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Abstract

Pairwise similarity mapping, implemented in the software PaSiMap, can be used as an alternative to principal component analysis (PCA) to analyse protein-sequence relationships. It provides the advantage of distinguishing between systematic and random differences in the dataset. Here, we present a protocol to use PaSiMap inside Jalview. You will be guided through the installation and use of the required software. Furthermore, we present an R script to prepare publication-ready graphs of the obtained data and aid in the subsequent data analysis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/621149v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1daf3d2org.highwire.dtl.DTLVardef@1bd82cborg.highwire.dtl.DTLVardef@d60c7aorg.highwire.dtl.DTLVardef@cd5a89_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Morell, T., Procter, J., Barton, G. J., Diederichs, K., Mayans, O., Fleming, J. R.. 2024-10-31. Sequence clustering with PaSiMap in Jalview. https://doi.org/10.1101/2024.10.30.621149

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