BIOLOGICAL SEQUENCE VARIANT CHARACTERIZATION

摘要

Short fixed length sub-sequences, defined as reference sub-sequences, are extracted from a collection of reference sequences, and an index is constructed showing which short fixed length reference sub-sequence occurs in which reference sequences. Short fixed length sub-sequences, the same length as the reference sub-sequences and defined as source sub-sequences, are extracted from a collection of source sequences derived from a sample for which the signature is to be determined, and the short fixed length source sub-sequences are compiled to determine the frequency of each within the collection. The presence or absence of source sub-sequences in combination with the index is used to infer the presence or absence of reference sequences from the reference collection.

主权项

1. A method for determining a signature from biological sequence data, comprising:
extracting short fixed length sub-sequences, defined as reference sub-sequences, from a collection of reference sequences, and constructing an index showing which short fixed length reference sub-sequence occurs in which reference sequences; extracting short fixed length sub-sequences, the same length as the reference sub-sequences and defined as source sub-sequences, from a collection of source sequences derived from a sample for which the signature is to be determined, and compiling the short fixed length source sub-sequences to determine the frequency of each within the collection; and using the presence or absence of source sub-sequences in combination with the index to infer the presence or absence of reference sequences from the reference collection; wherein one or more of the above steps are performed in accordance with a processor and a memory.