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visits member for 2 years, 1 month
seen Nov 14 at 8:15

I'm a bioinformatician with a background in evolutionary biology (mostly phylogeny).


Oct
4
awarded  Yearling
Sep
24
awarded  Autobiographer
Sep
17
comment How closely related are two parasites Giardia intestinalis and Trichomonas vaginalis?
Be careful though that Tolweb is not always very up-to-date.
Sep
9
comment Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)
Could it be that the bird was holding something into its beak, which made it look curved?
Sep
9
answered where to find the relative frequency distribution of synonymous codons
Aug
19
comment How do I perform recurring pattern mining or regular expressions of nucleotide sequences?
For python, the Bio.motifs package from BioPython could be useful: biopython.org/DIST/docs/tutorial/Tutorial.html#sec244
Jan
28
answered Insect identification
Dec
5
answered Cats, Dogs and Bears - how are they related?
Dec
5
comment Cats, Dogs and Bears - how are they related?
What do you mean by "paralogous clade"?
Nov
12
answered A wierd looking fish with a shield
Oct
25
comment Family tree for edible plants?
Beware that tolweb is not very accurate: from what I understood, they lack the funding necessary to update it. So it doesn't reflect the state of the art in terms of phylogeny.
Oct
4
awarded  Yearling
Sep
12
comment Molecular Evolution: Mrbayes never stops?
And if all what kmm suggests fail, it may be time to fiddle with finer tunings, such as concerning the proposals that are used to modify the Markov chain.
Sep
3
comment Could be an union/synergy between Math, Computer Science and Marine Biology?
I have the intuitive feeling that it may be easier to specialize in computer sciences and then apply this to marine biology than specialize in marine biology and then learn the computational tools. It may be easier to learn the tricky technical aspects with a younger brain, and later acquire the necessary knowledge to apply your technical skills to marine biology. Of course, it would be better if you could study both at the same time, but it may be difficult to arrange this.
Aug
13
comment Plant identification?
It would help if you provided more photos, such as a detail of the flower (where petals and other structural elements can be counted), the stem, the leaves, etc.
Jun
25
answered How do PLINK files and HapMap Phased files differ?
Jun
20
comment What do rs id, allele coded 0 and allele coded 1 mean?
@Alan Boyd Yes, I should have read the page further. So there is this "GRC human genome (build 37)" which is an artificial haploid reference. Is this the reference for all registered SNP? It could be but I have no certainty. One reason for my doubts is the following: Can it happen that a new SNP is identified in a portion of the genome not yet present in this reference genome? I suspect this is becoming rare, but when this reference was in earlier stages of construction, may be it could have happened.
Jun
20
awarded  Commentator
Jun
20
comment What do rs id, allele coded 0 and allele coded 1 mean?
@terdon is the reference genome the same for every registered SNP? I mean, if you took the 0 allele at every SNP registered with a rsID, would you end up with the genetic profile of one specific individual? It seems not: I read in en.wikipedia.org/wiki/Reference_genome that "the Genome Reference Consortium human genome (build 37) is derived from thirteen anonymous volunteers from Buffalo, New York". Is that the genome used as a reference for 0/1 labelling of SNPs? And what to do when there is polymorphism in this group of people? Maybe I could make a new question...
Jun
12
answered What flying insect is this?