dear Biostars,
I would like to obtain the hydropathy plots of several aligned protein sequences and display them in a similar manner to this BMC Evolutionary Biology paper
They state that they used EMBOSS pepwindowall (a web version is also available), but while that program is able to output several sequences it gets very messy since one cannot display each sequence analysed with a different colour. I have tried to locate alternative programs, but have failed so far.
I hope I do not have to perform separate runs, colour each using Photoshop and then overlay them ;)
all the best,
Golly
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1 answer
You can get a numerical plot of hydropathy using the Kyte-Doolittle program from:
http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1&pgm=tkd
pgm=tkd presents the data in numerical tabular format, which you can plot with excel, or some other plotting program.
Be careful about insertions/deletions in the multiple sequence alignment shifting the residue coordinates in the K-D plot.
Ignore the lines starting with '#'.
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I am not familiar with hydrophobicity plots and EMBOSS pepwindowall, but instead of outputting a graph directly from pepwindowall, may be you can output the results in "data" format using the offline version and create plots of your own using R or excel.