Protists homology analysis

Question

[agata88]

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

Answer 1

[h.mon]

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.

[agata88]

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