Spliced alignments

Mott, R. (1997). EST GENOME a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci. 13, 477—478. 

Incompletely spliced primary messenger, as well as unprocessed genomic material, may be present as impurities in a mRNA preparation and may obscure the alignment of autologous ESTs necessary for finding variants. 

Analysis of the base sequence of the rRNA precursor suggested that the 5 splice site is aligned with the catalytic residues by base-pairing between a pyrimidine-rich region (CUCUCU) of the upstream exon and a purine-rich guide... 

Most striking is the splicing of mRNA precursors, which is catalyzed by spliceosomes consisting of small nuclear ribonucleoprotein particles (snRNPs). The small nuclear RNA (snRNA) molecules in these complexes play a key role in directing the alignment of splice sites and in mediating catalysis. Indeed, some RNA molecules can splice themselves in the absence of protein. This landmark discovery by Thomas Cech and Sidney Altman revealed that RNA molecules can serve as catalysts and greatly influenced our view of molecular evolution. 

Gelfand M., MironovA., Pevzner P. (1996) Gene recognition via spliced sequence alignment. Proc Natl Acad Sci USA, 93, 9061-9066. 

Brendel, V., L. Xing, and W. Zhu. 2004. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20 1157-69. 

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