Ab initio generation of single copy genomic probes

One or more tangible computer-readable storage media having computer-executable components for identifying a single copy sequence in a target reference complete genome sequence, said components comprising:

• a first genome comparison component for determining a count of the number of times a subsequence of a first screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence obtained by division of the target reference genome sequence, wherein the target reference genome sequence comprises the first screened sequence, the first screened sequence is divided into at least two subsequences, and a subsequence of the first screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the first screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the first screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the first screened sequence or the group of contiguous subsequences of the first screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• a second genome comparison component for determining a count of the number of times a subsequence of a second screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence, wherein the second screened sequence comprises a single copy interval of the first screened sequence;
• the second screened sequence overlaps the single copy interval of the first screened sequence;
• the subsequences of the first screened sequence are either (i) consecutive non-overlapping subintervals of the second screened sequence or (ii) overlapping non-identical subintervals of the second screened sequence, and a subsequence of the second screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the second screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the second screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the second screened sequence or the group of contiguous subsequences of the second screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• and
• a subsequence component for identifying a single copy interval as a single copy sequence of the target reference sequence suitable for use as a single copy hybridization probe;
• and wherein the results achieved from the computer-executable components of the computer-readable storage media are outputted in a user readable format.

A computerized system for identifying a single copy sequence in a target reference complete genome sequence, said computerized system comprising a computer-readable storage media, said computer-readable storage media comprising:

• means for determining a count of the number of times a subsequence of a first screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence obtained by division of the target reference genome sequence, wherein the target reference genome sequence comprises the first screened sequence, the first screened sequence is divided into at least two subsequences, and a subsequence of the first screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the first screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the first screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the first screened sequence or the group of contiguous subsequences of the first screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• means for determining a count of the number of times a subsequence of a second screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence, wherein the second screened sequence comprises a single copy interval of the first screened sequence;
• the second screened sequence overlaps the single copy interval of the first screened sequence;
• the subsequences of the first screened sequence are either (i) consecutive non-overlapping subintervals of the second screened sequence or (ii) overlapping non-identical subintervals of the second screened sequence, and a subsequence of the second screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the second screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the second screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the second screened sequence or the group of contiguous subsequences of the second screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• and
• means for identifying a single copy interval as a single copy sequence of the target reference genome sequence suitable for use as a single copy hybridization probe;
• and wherein the single copy sequence is outputted in a user readable format.

A method to prepare a single copy hybridization probe from a target reference complete genome sequence by successive division of the target reference genome sequence into subintervals and comparison the subintervals to the target reference sequence, said method comprising:

• determining a count of the number of times a subsequence of a first screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence obtained by division of the target reference genome sequence, wherein the target reference genome sequence comprises the first screened sequence, the first screened sequence is divided into at least two subsequences, and a subsequence of the first screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the first screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the first screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the first screened sequence or the group of contiguous subsequences of the first screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• determining a count of the number of times a subsequence of a second screened sequence occurs in the target reference genome sequence, said screened sequence being at least one subinterval of the target reference genome sequence, wherein the second screened sequence comprises a single copy interval of the first screened sequence;
• the second screened sequence overlaps the single copy interval of the first screened sequence;
• the subsequences of the second screened sequence are either (i) consecutive non-overlapping subintervals of the second screened sequence or (ii) overlapping non-identical subintervals of the second screened sequence, and a subsequence of the second screened sequence with a single subsequence occurrence in the target reference genome sequence or a group of contiguous subsequences of the second screened sequence each with a single subsequence occurrence in the target reference genome sequence is identified as a single copy interval of the second screened sequence, wherein an occurrence is defined by at least about 50 consecutive nucleotides of the subsequence of the second screened sequence or the group of contiguous subsequences of the second screened sequence displaying (i) at least about 60% homology to the target reference sequence;
• (ii) at least about 70% homology to the target reference sequence;
• or (iii) at least about 80% homology to the target reference sequence;
• identifying a single copy interval as a single copy sequence of the target reference sequence suitable for use as a single copy hybridization probe;
• and
• preparing a single copy hybridization probe comprising a single copy sequence.