[Right Wing Professor]

I used Blast to search out, using Ciona intestinalis, similar sequences. You can see from my listing that fish ADH3 is closer than the other 2 species used in your citation. Why is that, in light of your assertion?

You have to be careful comparing sequences, particularly fairly distantly related ones. BLAST is generally used for searching for related sequences; other methods are generally used for doing quantitative comparisons.

I pulled up three sequences; Ciona ADH3, Branchistoma floridae (a cephalohordate) ADH3, and Danio (zebrafish) ADH (number not specified) Here is the N terminus amino acid sequence:

C -GKVINCSAAVAWG...P...KKP.....-..-LS.IE....K..I..QVA.....PP.....K.....A.....HEV...RIK..VMAT.GVC.HTDAFTLSGEDP.....EAAFP.....VILGHEG.
B AGKPISCRAAVAWE...A...KKP.....-..-LV.IE....T..I..EVA.....PP.....K.....A.....HEV...RIK..VLAT.GVC.HTDAYTLSGADS.....EGKFP.....VVLGHEG.
D AGKVIKCRAAVAWE...P...KAP.....-..-LM.ME....E..I..EVA.....PP.....Q.....E.....GEI...RIK..VIAT.GLC.HTDLYHLVDGDK.....-RGFP.....VVLGHES.

Without weighting particular kinds of substitutions, I get 16 mismatches between Ciona and Branchiostoma, 23 mismatches between Ciona and Danio, and 27 mismatches between Branchiostoma and Danio. Of course, you'd really want to do this over the whole genome, not one end of one protein; I think the pros weight some mismatches more heavily than others; and this is a really tough example, because probably all three lines diverged at nearly the same time a long time ago.

I am impressed, though. There are damn few non-specialists who would go look at the raw data as you have.

[f.Christian]

Intelligent -- logical people are starting to see // understand ...

that science // physics are 'stable' ---

and evolution (( sociological )) is flux --- opposites --- ideology (( political )) !

[AndrewC]

Without weighting particular kinds of substitutions, I get 16 mismatches between Ciona and Branchiostoma, 23 mismatches between Ciona and Danio, and 27 mismatches between Branchiostoma and Danio.

First, thanks for the kind words. Now, I disagree with using the whole genome, due to the additions and deletions of genes and the fact that there are different time factors involved in the changes. So it seems to me a better indicator to select a fairly constant gene(actually the end product) and compare them. I selected the ADH3 protein from Ciona (AAL72131) and let Blast give me the answer. I used a 377aa sequence. The program evidently takes the weighted substitutions to give a score. How it arrives at the final number is a bit unclear since in the previous data Danio was given a higher score (1370) than Sparus (1369) even though in the following data Sparus has more (296) positive matches than Danio (295).

• Danio rerio Identities = 257/376 (68%), Positives = 295/376 (78%)
• Sparus aurata Identities = 257/376 (68%), Positives = 296/376 (78%)
• Branchiostoma floridae Identities = 256/377 (67%), Positives = 292/377 (77%)
• Gadus morhua Identities = 253/374 (67%), Positives = 289/374 (77%)
• Anopheles gambiae str. PEST Identities = 254/375 (67%), Positives = 291/375 (77%)
• Indian spiny-tailed lizard Identities = 250/373 (67%), Positives = 292/373 (78%)
• Branchiostoma lanceolatum Identities = 250/377 (66%), Positives = 288/377 (76%)

You can also see that the program searches for a match within each sequence because not all have 377 as a "denominator". Adjusting for that will not change the order(even though the lizard has one more positive than the mosquito it has four less identities.) You can subtract each positive from 377 to calculate your mismatch number