Method and computer software product for genomic alignment and assessment of the transcriptome
AssigneeAffymetrix, Inc.
InventorsAlan Williams, Simon Cawley, Raymond Wheeler, Brant Wong, David Kulp
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Abstract
In one embodiment of the invention, computerized methods are provided for analyzing transcript sequence clusters by aligning the transcripts with genomic sequences to determine whether a cluster needs to be sub-clustered and whether clusters should be merged. In addition, in some embodiments, transcript sequences are trimmed according to their alignment with their corresponding genomic sequences. The modified clusters and trimmed sequences may be used for nucleic acid probe array design.
Claims50
A method for analyzing a plurality of transcript sequences in a cluster comprising:
- aligning the transcript sequences with genomic sequences;
- and
- determining whether the clusters need to be modified according to the aligning.
A method for triming a transcript sequence comprising:
- aligning the transcript sequence to its corresponding genomic sequence;
- removing a side sequence of the transcript sequence if the side is poorly aligned with the genomic sequence.
A method of designing a nucleic acid probe array comprising:
- aligning a plurality of transcript sequences in a cluster to their corresponding genomic sequence;
- modifying the clusters according to their aligning to the genomic sequence to obtain at least one modified cluster;
- and
- selecting probes targeting the at least one modified cluster.
A method of designing a nucleic acid probe array comprising:
- aligning a transcript sequence to its corresponding genomic sequence;
- triming a side of the transcript sequence to obtain a trimmed transcript sequence if the side of the transcript sequence is poorly align with the genomic sequence;
- and
- selecting probes targeting the trimmed transcript sequence or clusters including the trimmed transcript sequence.
A computer readable medium comprising computer-executable instructions for performing the method comprising:
- aligning transcript sequences from a cluster with genomic sequences;
- and
- determining whether the clusters need to be modified according to the aligning.
A computer readable medium comprising computer-executable instructions for performing the method comprising:
- aligning a transcript sequence to its corresponding genomic sequence;
- removing a side sequence of the transcript sequence if the side is poorly aligned with the genomic sequence.
A computer readable medium comprising computer-executable instructions for performing the method comprising:
- aligning a plurality of transcript sequences in a cluster to their corresponding genomic sequence;
- modifying the cluster according to their aligning to the genomic sequence to obtain at least one modified cluster;
- and
- selecting probes targeting the at least one modified cluster.
The computer readable medium of claim 42 wherein the step of modifying comprises subclustering a chimeric cluster.
A computer readable medium comprising computer-executable instructions for performing the method of
- aligning a transcript sequence to its corresponding genomic sequence;
- triming a side of the transcript sequence to obtain a trimmed transcript sequence if the side of the transcript sequence is poorly align with the genomic sequence;
- and
- selecting probes targeting the trimmed transcript sequence or clusters including the trimmed transcript sequence.
Dependencies are inferred from the claim text.