[ssml] Standard for comparing nucleotide alignments

Kevin Karplus karplus at soe.ucsc.edu
Thu Dec 11 22:36:39 EST 2003

If you are just looking for something the quality of BaliBase, you can
make up whatever alignments you like.  Balibase is NOT gold-standard quality.
It is long past time to discard Balibase and create a better alignment

Getting reliable nucleotide alignments for protein-coding sequences is
not too hard (use a good protein alignment, then look up the original
DNA), but for non-coding DNA, getting experimental validation of
alignments is extremely difficult.  You can get some ribosomal RNA
alignments that are pretty good, that use the secondary structure as
well as the primary structure in making the alignments.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.

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