Appeal No. 2006-1569 Page 3
Application No. 10/159,997
Discussion
1. Claim construction
Claims 1-4 are pending and on appeal. Claim 1 is the only independent claim
and reads as follows:
1. A computational method for systematically identifying alternative mRNA
splice isoforms of known genes, the method comprising the steps of:
a) identifying target gene sequences by mapping mRNA sequences of an
mRNA sequence dataset to genomic sequences of a genomic DNA
sequence dataset, wherein:
each mRNA sequence is required to align to a corresponding genomic
sequence over the full length of the coding sequence of the mRNA
sequence, without gaps in the exons of the genomic sequence; and
at least 98% identity between each mRNA sequence and the
corresponding genomic sequence is required, favoring the mRNA
sequence in case of nucleotide mismatch; and
b) identifying a dataset of alternate mRNA splice isoforms of the target
gene sequences by aligning EST sequences from an EST sequence
dataset to the target gene sequences and using a transcript assembly
protocol, wherein:
the alternative mRNA splice isoform dataset is restricted to mRNA
sequences in which the 5' end of an EST sequence aligns to a coding
sequence of the corresponding mRNA sequence, such that the reading
frame of the coding sequences can be determined for all isoforms of the
dataset, and
isoforms presenting intron retention are excluded from the alternative
mRNA splice isoform dataset, and
coverage by multiple EST sequences is required for each splicing event.
Thus, claim 1 is directed to the exemplary embodiment of the disclosed protocol
discussed on pages 3-4 of the specification, with the exception that claim 1 is not limited
to use of the RefSeq and dbEST databases.
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