Analyzing .fasta file.

Question

[jaqx008]

Hey guys. I need some help. I have obtained some amino acid sequences (Mostly Argonaut family proteins) from humans, c. elegans and drosophila. I tried to find hits of the a.a sequencings in two other organisms. Hoping that with this I can draw some conclusions based on the Argonaut or other protein members. I have fasta format hits generated but Im having the following difficulties or confusions:

1. the sequences in the faster files are too large for some of the proteins. I don't know what to make of the regions generated if they correspond to the proteins in the two organisms genome.
2. Were do I go from here in other to establish an evolutionary relationship or divergence. I haven't work on any evolutionary tree or phylogenetic tree before. I would like your help and suggestions please.

Thanks

[GenoMax]

Not answering your question directly since you can find good examples for this sort of thing. One example is from MEGA software.

Have you checked NCBI's Homologene site? They may have already done the work for you.

[jaqx008]

This really does not help me. I don't understand whats on the MEGA page or what it does. the Homologene site makes some sense, but still doesn't help. what am I searching for on here. Im trying to do this thing and hopefully learn from it.

[h.mon]

See my answer to your other, similar post:

[natasha.sernova]

What I’ve found:

The protein family was very well studied some time ago. Thare is an interesting domain here.

To find it you need to aligh protein sequences with muscle or mafft.

https://www.ebi.ac.uk/Tools/msa/muscle/

As to your tree, see the post below:

Plylogenetic tree construction

You can search for orthologous protein, using OMA or orthodb tools.

https://omabrowser.org/oma/home/

OR use orthodb:

http://www.orthodb.org/

This protein family can be encountered in many organisms. This is its evolution, isn't it?

https://en.wikipedia.org/wiki/Argonaute

https://en.wikipedia.org/wiki/Piwi

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374724/

http://www.cell.com/structure/fulltext/S0969-2126(05)00305-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0969212605003059%3Fshowall%3Dtrue

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743648/

http://pfam.xfam.org/family/pf02170

http://www.abcam.com/research-areas/focus-on-argonaute-proteins

Look at these articles above, see some similar posts on the right panel, like the one below.

Finding novel domains in a group of proteins

[jaqx008]

Ok. Thanks. I will take a look at them.