501 reputation
28
bio website about.me/gawbul
location London, United Kingdom
age 33
visits member for 2 years, 7 months
seen Jan 19 '13 at 4:53

Dad and husband. Passionate about science, research, computing, and all things geeky :D


Jun
10
comment Did animals evolve from plants?
Thanks for the comments @RichardSmith :) I have updated my post accordingly.
May
7
comment Did animals evolve from plants?
Here's a cool phylogenomics paper by Eugene Koonin "The origin and early evolution of eukaryotes in the light of phylogenomics" - genomebiology.com/2010/11/5/209
May
7
comment Did animals evolve from plants?
As I mentioned in my post, resolving the relationships of the organisms at the base of the phylogenetic tree is particularly difficult. I'm all for taking a multi-gene phylogenomic approach to this, but the more genes we add the more computationally intensive the analysis. Also, incomplete lineage sorting and other issues can compound resolution of the tree. I should imagine these things were so similar, that determining relationships is even more difficult. As we have no sequences for these organisms, we must perform ancestral state reconstruction in order to, infer the hypothetical nodes.
May
7
comment Did animals evolve from plants?
Edited my question to include chloroplast origin information. Hope that helps?
May
7
comment Did animals evolve from plants?
Ancestors of animals had mitochondria (hence the "animal equivalent of the chloroplast is the mitochondria), as did the ancestors of plants have chloroplasts. Although, it is a common misconception, that plants don't respire and in fact most plants also have mitochondria.
Dec
14
comment What are the limiting factors for gene length and number of exons?
Dystrophin is the longest gene, but doesn't encode the longest product, which of course is Titin. 363 exons is one hell of number! Lol :)
Dec
14
comment What are the limiting factors for gene length and number of exons?
Talking about annotation quality control, one needs to think about the molecular constraints on the size of an exon, or intron for that matter. The (theoretical) minimum length of an exon would have to 1bp, although one would also need to think about the binding of molecular machinery involved in exon-intron boundry recognition and the splicing of adjacent exons. I should think exons of less than 6bp would probably not be considered functional? See jbc.org/content/270/6/2411.full and mbe.oxfordjournals.org/content/23/12/2392.full
Dec
14
comment What are the limiting factors for gene length and number of exons?
The EnsEMBL Perl API is a cool way to retrieve the precise data you need - ensembl.org/info/docs/api/index.html
Dec
14
comment What are the limiting factors for gene length and number of exons?
How did you retrieve the genes/exon annotations? BioMart, or EnsEMBL API?