Nucleic Acids Research, Vol 27, Issue 13 2627-2637, Copyright © 1999 by Oxford University Press
TA Thanaraj
A clean data set of verified splice sites from Homo sapiens are reported as
well as the standards used for the clean-up procedure. The sites were
validated by: (i) standard cleaning procedures such as requiring
consistency in the annotation of the gene structural elements, completeness
of the coding regions and elimination of redundant sequences; (ii)
clustering by decision trees coupled with analysis of ClustalW alignments
of the translated protein sequence with homologous proteins from
SWISS-PROT; (iii) matching against human EST sequences. The sites are
categorised as: (i) donor sites, a set of 619 EST-confirmed donor sites,
for which 138 are either the sites or the regions around the sites involved
in alternative splice events; (ii) acceptor sites, a set of 623
EST-confirmed acceptor sites, for which 144 are either the sites or the
regions around the sites are involved in alternative splice events; (iii)
genuine splice sites, a set of 392 splice sites wherein both the donor and
acceptor sites had EST confirmation and were not involved in any
alternative splicing; (iv) alternative splice sites, a set of 209 splice
sites wherein both the donor and acceptor sites had EST confirmation and
the sites or the regions around them were involved in alternative splicing.
A set of nucleotide regions that can be used to generate a control set of
false splice sites that have a high confidence of being non-functional are
also reported.
ARTICLES
A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. thanaraj@ebi.ac.uk
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