[Taxacom] molecular data challenges

John Grehan jgrehan at sciencebuff.org
Tue Nov 11 08:01:33 CST 2008


I'm finding that I am running into a new problem with accessing
molecular data. It seems that rather than presenting the actual aligned
data as in earlier papers, electronic versions are being stored in
zipped files that require the right software not only to open them, but
also to align the data itself - at least that's my understanding in one
case. The problem here is that if one does not use the original
alignment algorithm then one may not get the same homologies. 

 

With respect to the Prasad et al (2008) data, apparently the files I
opened produced a different result from what is supposed to be contained
in the files (A colleague of mine opened the original coding.fa and
cons_noncode.fa using Clustal-x. I then read the data on PAUP in order
to be able to print it out, but it seems to have been different from
what was supposed to be in the file.

 

The author has advised me that I need to open the files using jalview
(http://www.jalview.org/). Unfortunately I am not that computer savvy so
I don't know if I will be able to figure out how to work the software
(my first attempt produced &&%%%4#@ sort of stuff. This brings me back
to my main concern, that the raw data is not openly accessible, but
requires a certain amount of computational knowledge to generate the
data. Any comments on this? (but no comments on my IQ please).

 

I asked the author for a copy of the aligned data and am waiting to hear
back.

 

John Grehan

 

 

 

Dr. John R. Grehan

Director of Science

Buffalo Museum of Science1020 Humboldt Parkway

Buffalo, NY 14211-1193

email: jgrehan at sciencebuff.org

Phone: (716) 896-5200 ext 372

 

Panbiogeography

http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php

Ghost moth research

http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php

Human evolution and the great apes

http://www.sciencebuff.org/human_origin_and_the_great_apes.php

 

 




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