October 1, 2007 (Vol. 27, No. 17)


Strong Points: Useful predictions
Weak Points: Not perfect

Take a genomic eukaryotic sequence, match it with a mature eukaryotic mRNA or a reverse-translated protein sequence, and you’ll discover the location of introns. These, of course, are spliced out during RNA maturation. If you remember anything from the last review, you’ll recognize that splicing is a many splendored thing that can take many paths for a given gene. But, you may interject, how can I predict the multiple alternative splices that might occur if all I have is a sequence? To the rescue comes ASmodeler, an online system for doing this dirty work. Sequence entry is easy. Users can specify genomic sequences by UniGene ID number and then either paste in mRNA, EST, or Protein sequence or, alternatively, upload a file with sequence info. Numerous modeling methods for predicting alternative splice sites are available. Is the system perfect? No, many splices are predicted that are not known to occur biologically, so the program is best used as a theoretician’s tool. Still, ASmodeler is a very useful and powerful program for molecular biologists.

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