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phylogenetic distribution of a domain

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phylogenetic distribution of a domain

Postby turlaa » Thu Apr 15, 2010 8:39 pm

Firstly I have to say i am NOT talented in bioinformatics-but I try=)
I have to search for a certain domain in actinobacteria. I have the results but I dont know how to plot a tree or how to present them in any other way. I have to show if the tree of this protein resemble phylogenetic tre of bacteria-any ideas?
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Postby JackBean » Thu Apr 15, 2010 8:45 pm

Are you looking for the primary or tertiary structure? For primary structure just use ClustalW or T-Coffee. Or tertiary structure you should use some 3D alignment (Dali search?)

After that you should just make some tree by some method and visualize in TreeView.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby turlaa » Thu Apr 15, 2010 8:48 pm

I did it in ClustalW but it was only showing gene object ID and I wanted elaborate bout product and genome name. So i don't think that this one will work.
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Postby turlaa » Thu Apr 15, 2010 8:54 pm

so my problem is that it can't be any tree but a tree showing right data and I wonder if there is any program where I can create tree from my data(sequence +name of product +name of species=fasta) and create phylogenetic tree of organism with proteins showed on it
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Postby JackBean » Thu Apr 15, 2010 9:52 pm

I don't get this one much. What do you mean by "showing only gene ID"? There should be some multiple alignment
http://www.biolib.cz/en/main/

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Postby turlaa » Thu Apr 15, 2010 9:57 pm

well I would love to have tree like that
http://www.scielo.br/img/revistas/bjm/v39n2/a35fig1.gif 9random from google)
not like http://www.google.co.uk/imgres?imgurl=h ... s%3Disch:1 but since mega is not working I'm not having much choice
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Postby turlaa » Thu Apr 15, 2010 9:58 pm

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Postby JackBean » Fri Apr 16, 2010 7:20 am

I'm sorry, but what's the difference?
http://www.biolib.cz/en/main/

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Postby turlaa » Fri Apr 16, 2010 1:02 pm

well I have protein sequences and I obtain trees with branches names as protein Id 9in some programs when i place arrow on branch it tells me what organism it belongs to but not alway) an i would want to have organism name visible. So I look for program which allow me to build a tree and choose which data is going to be included on the tree. I hope it's clear. One more time thank you for your help
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Postby JackBean » Fri Apr 16, 2010 2:24 pm

I see :)

well, you have two options:
you have your sequences in some fasta format or something like that? IMHO you should be able just add the name of the species. But the space may be problem, so use "_" instead (Shift + "-"), so you will have e.g. 2ZE5_Agrobacterium_tumefaciens ;) The question is, how long can your ID be ;)
the other way is simply just to rewrite it in some picture editor ;) (Like Photoshop or something similar)
http://www.biolib.cz/en/main/

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Re: phylogenetic distribution of a domain

Postby turlaa » Fri Apr 16, 2010 3:45 pm

for future underdeveloped ppl like me. I puted my fasta to clustalw on align.genome.jp webpage what allowed me to aling (huge amount of data) saved it in aln format and created tree I could save in pdf(if you create big trees on ebi web page clustal you only see part) an I have a few styles to choose. An now mega is somehow consuming my data!
:mrgreen: Thank you for your help! I can't imagine finishing this without you! :mrgreen:
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Re: phylogenetic distribution of a domain

Postby viki78 » Wed Jul 13, 2011 1:35 pm

I have the same problem unfortunately
but i really need it :(
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