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Protists homology analysis

Hi all!

Which tool would you recommend for analysis of few aa protists sequences for:

  • searching for homologues,

  • prediction of signal/transit peptides,

  • phylogenetic analysis,

  • searching for alternative translation sites,

Thanks in advance!

Best, Agata

protists homology
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updated by h.mon h.mon • written by agata88 agata88

1 answer

You should explain in more detail your data, as suggestion will depend on what data do you have and how it is organized.

  • searching for homologues

If you have amino-acid sequences from various species, then you can use PorthoMCL or OMA or ProteinOrtho. If you have sequences from just one species, you can look at orthology databases - see a list at List of orthology databases.

  • prediction of signal/transit peptides

I don't know of any protist-specif tools, but you can use SignalP or Phobius, among others. It seems the best results are obtained using a combination of several tools.

  • phylogenetic analysis

Align with muscle or mafft, reconstruct phylogeny with RAxML.

  • searching for alternative translation sites

You can't search for alternative translation sites if all you have are amino-acid sequences.

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written by h.mon h.mon

Thanks! I will try it all. What tool would you recommend for searching for alternative translation sites with nucleotide transcript sequences?

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written by agata88 agata88

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