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  1. Anonymous

    After attending the ASPB seminar, I tried the phylogenes. It is a wonderful and handy tool but I have some questions:


    (1) There are limited options to search for a novel gene. E.g. I tried searching the Arabidopsis SWEET gene (At1g21460) which has 17 orthologues in Arabidopsis and about 52 homologs in soybean. However, this search does not result in the same number of genes.

    (2) Moreover, the naming on genes is not consistent in the phylogenetic tree. e.g. at some places, it gives gene id (At1g21460) while some places it names SWEET6 etc. etc.

    (3) Is there any way we can use the protein/dna sequence to blast > see gene function > built tree?

    (4) different types of tree (circular), for publication purposes. 

    (5) obtain gene/protein sequence?



  2. Peifen Zhang

    Dear PhyloGenes's user, 

    Thank you for the valuable feedback! I will reply to a few of them here:

    1) All search in PhyloGenes returns gene families, not genes. Perhaps that caused the confusion? 

    Some AGI IDs are not searchable, i.e.  At1g21460. This is a known issue. We are fixing it. The fix should become available very soon.

    If you search 'sweet1' (At1g21460), you will find it in this gene family, http://www.phylogenes.org/tree/PTHR10791. 

    If you click on the operation menu icon (the wrench) above the tree graph and choose 'prune tree by organisms', you could select to see only Arabidopsis and soybean genes on the tree (a pruned view). In that 'prune tree by organisms' popup window you can also easily see how many genes of each species are included in the gene family. In this case, 18 Arabidopsis genes and 53 soybean genes.  

    Only genes with experimentally supported functional annotations are shown in the default tree view. Remember to click on the 'Expand All' icon above the tree graph to see all genes in the tree. 

    2) In the gene family that contains sweet1, all Arabidopsis genes on the tree are labeled with their symbols including sweet1 (for At1g21460). It is strange that you are somehow seeing differently. Could you email us a screen shot (info@phylogenes.org)?

    3) From the home page, http://www.phylogenes.org/, the right side pane lists genomes included in the gene family build. There is a button 'Not seeing your species'. Clicking it will take you to the TreeGrafter, a feature that one can copy/past a protein sequence to graft it to a matching gene family. Is it the kind of function you were asking for?

    4) We don't have the circular tree feature. Will consider it in the future. In the mean time, you could download the tree in PhyloXML format and open/edit in another software such as iTOL or EvolView.

    5) Yes, we are planning to provide a feature to download protein sequences of a gene family.  


  3. Anonymous

    Peifen,


    Thanks for the reply. I have sent you the phylogeny screenshot to info@phylogenes.org. 

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