RT Journal
A1 Volfovsky, Natalia
A1 Haas, Brian J.
A1 Salzberg, Steven L.
T1 Computational Discovery of Internal Micro-Exons
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6a 
SP 1216 
OP 1221 
DO 10.1101/gr.677503 
UL http://genome.cshlp.org/content/13/6a/1216.abstract 
AB Very short exons, also known as micro-exons, occur in large numbers in some  eukaryotic genomes. Existing annotation tools have a limited ability to  recognize these short sequences, which range in length up to 25 bp. Here, we  describe a computational method for the identification of micro-exons using  near-perfect alignments between cDNA and genomic DNA sequences. Using this  method, we detected 319 micro-exons in 4 complete genomes, of which 224 were  previously unknown, human (170), the nematode Caenorhabditis elegans
 (4), the fruit fly Drosophila melanogaster (14), and the mustard  plant Arabidopsis thaliana (36). Comparison of our computational  method with popular cDNA alignment programs shows that the new algorithm is  both efficient and accurate. The algorithm also aids in the discovery of  micro-exon-skipping events and cross-species micro-exon conservation.