[Bioperl-l] Homology/Phylogeny pretty-print for non-bioinformatics researchers

[Will Spooner]

Hi Robert,

Speaking for Ensembl, the GeneTree display code is deeply embedded in  
the API and web code, and refactoring as a standalone package would be  
exceedingly difficult. Jalview (http://www.jalview.org) may be a good  
alternative, albeit a Java one. There is code available for driving  
Jalview from the Ensembl database, and something similar for BioPerl  
seems reasonable.

Will

On 17 Aug 2009, at 18:14, Robert Bradbury wrote:

> One of the questions facing people working in bioinformatics is "How  
> do we
> present information so that it can be effectively interpreted by
> non-informatics specialists?"
>
> Now, my expertise lies in computer science (esp. O.S. & databases)  
> and as a
> second vocation the biology of aging (DNA damage & repair, to a lesser
> extent cancer and pathologies of aging, etc.).  Now by my estimate  
> there are
> perhaps 5 people in the world who are able to effectively discuss  
> computer
> science X aging (gerontology) [3].  There are perhaps several dozen  
> people
> where those areas, esp aging, may overlap with DNA damage & repair.   
> But
> then there is a wider audience of perhaps a few hundred members of  
> AGE, and
> maybe a thousand or so who are members of the scientific subgroup of  
> GSA.
> But most of those individuals are "old school" scientists who know
> relatively little about bioinformatics.  So one has barriers to  
> presenting
> bioinformatics information in ways that they can use usefully.
>
> I have found in my limited experience that homology graphs of  
> conserved
> protein domains, such as those displayed in HomloGene or those in  
> Ensembl
> (including phylogeny graphs) can be quite useful in reaching  
> interesting
> conclusions.  For example, double strand break repair processes  
> which may
> involve 8-10 relatively conserved proteins, may have a critical role  
> in the
> mechanisms of aging.  In particular two of those proteins, WRN &  
> DCLRE1C
> (Artemis) contain complementary exonuclease activities which chew up  
> the DNA
> in order to prepare the strands for ligation.  Of course,  
> programmers may
> appreciate better than gerontologists the significance of deleting  
> random
> bytes from instruction sequences in ones code.  At the recent AGE  
> meeting in
> June several discussions arose as to possible differences in "aging"  
> in
> yeast, *C. elegans* and mammals. [1].  A quick database search  
> showed that *C.
> elegans* seems to be lacking the exonuclease domain on the WRN  
> homologue and
> may be missing a DCLRE1C homologue entirely (which if true would  
> lead to
> conclusions that aging in *C. elegans* may be fundamentally  
> different from
> aging in vertebrates).  Explaining this to researchers can best be  
> done
> using pictures.
>
> I've been through PubMed and have several papers (NAR / BMC  
> Bioinformatics)
> regarding programs to do homology comparisons and phylogeny trees.   
> However
> these seem to lean towards producing less condensed bioinformatics-ish
> information.  I do not know however whether the outputs from  
> databases like
> PubMed HomoloGene or Ensembl have been packaged in tools that might  
> be part
> of BioPerl.  I am interested in programs that can be run on a  
> regular basis
> to draw "pretty pictures" that can be used for publication and/or  
> internet
> browsing.  In particular I'm interested in running such programs on  
> species
> of interest to various gerontological communities [2] which involves  
> subsets
> of databases which seem to be scattered around the world.
>
> Thanks.
>
> 1. Of course there has been lots of discussion and rationalization  
> over the
> last 15+ years about how "aging" is largely the same in more complex  
> and
> simpler organisms -- in part to justify sequencing some organisms  
> and in
> part to justify funding research at certain laboratories.  A closer
> examination based on some of the complete and emerging genome  
> sequences may
> suggest this is a very swampy discussion.
> 2. For example, nematode DNA repair gene comparisons would be  
> interesting to
> nematode researchers, insect DNA repair gene comparisons to insect
> researchers, both to invertebrate researchers, etc.
> 3. The recently published textbooks *Aging of the Genome* by Jan  
> Vijg and
> the 2nd edition of *DNA Repair and Mutagenesis* by Errol Friedberg  
> *et al*,
> go a long way towards moving these areas from the stacks of research
> libraries into areas for more general discussion.  Both volumes deal
> extensively with the ~150 DNA repair genes.
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com