Association of data to a biological sequence

Abstract

A computer assembly includes a processor configured to access data on a network and to perform a method. The method includes identifying, in the network, one or more references having a relevance level greater than a predetermined threshold. The one or more references are associated to one or more probe sequences corresponding to one or more biological sequences. The one or more probe sequences are ranked based on one or more criteria corresponding to a target biological sequence. The one or more probe sequences are assigned with a level of affinity to one or more segments of the target biological sequence based at least on the ranking of each of the one or more probe sequences.

1 . A computer assembly for associating data with a target biological sequence, comprising:
 a processor configured to access data on a network and to perform a method, the method comprising:   identifying, in the network, one or more references having a relevance level greater than a predetermined threshold, said references being at least one of a pointer and an address indicating a location of data or providing information regarding the data;   associating each reference of the one or more references to one or more probe sequences corresponding to one or more biological sequences;   ranking the one or more probe sequences based on one or more criteria corresponding to a target biological sequence; and   assigning the one or more probe sequences with a level of affinity to one or more segments of the target biological sequence based at least on the ranking of each of the one or more probe sequences.   
     
     
         2 . The computer assembly of  claim 1 , wherein the references are uniform resource locators (URLs). 
     
     
         3 . The computer assembly of  claim 1 , wherein associating the one or more probe sequences to the one or more references having a relevance level greater than a predetermined threshold includes analyzing the one or more references to detect the presence of one or more of key words, phrases, symbols and sources of the one or more references. 
     
     
         4 . The computer assembly of  claim 1 , wherein associating each reference of the one or more references to one or more probe sequences includes associating each reference with a biological sequence that is complementary to a biological sequence referenced by the reference. 
     
     
         5 . The computer assembly of  claim 1 , wherein ranking the one or more probe sequences comprises determining a similarity between the one or more probe sequences and the one or more segments of the target biological sequence, and
 ranking the one or more probe sequences further comprises at least one of determining an importance of a source of each reference of each probe sequence, determining a popularity of each reference of each probe sequence, and determining a historical applicability of each reference of each probe sequence to the one or more segments of the target biological sequence.   
     
     
         6 . The computer assembly of  claim 5 , wherein determining the similarity between the one or more probe sequences and the one or more segments of the target biological sequence includes determining a match between the one or more probe sequences and a complement of the one or more segments of the target biological sequence. 
     
     
         7 . The computer assembly of  claim 6 , wherein the method further comprises associating the one or more probe sequences with at least one of a document, an analysis tool, and biographical information of a person. 
     
     
         8 . The computer assembly of  claim 7 , wherein determining an importance of a source of each reference includes at least one of determining a number of citations of an author of the document, determining an organization to which an author of the document belongs, and determining a type of analysis performed by the analysis tool,
 determining a popularity of each reference includes at least one of determining a number of citations of the document and a frequency of use of the analysis tool, and   determining a historical applicability of each reference includes at least one of determining a frequency with which the document has been cited in association with the segment of the target biological sequence and determining a frequency with which the analysis tool has been used to analyze the segment.   
     
     
         9 . The computer assembly of  claim 1 , wherein the one or more probe sequences includes at least two probe sequences corresponding to a same segment of the target biological sequence, and
 assigning the at least two probe sequences a level of affinity to the segment of the target biological sequence includes competitively comparing the at least two probe sequences such that a reference having a higher ranking is assigned a higher level of affinity than a reference having a lower ranking.   
     
     
         10 . The computer assembly of  claim 1 , further comprising a display,
 wherein the method further comprises displaying a graphical representation of the segment of the target biological sequence on the display, and displaying a graphical representation of the level of affinity of each probe sequence to the segment of the target biological sequence on the display by adjusting a physical distance of a graphical representation of the probe sequence from the graphical representation of the segment based on the level of affinity of the probe sequence.   
     
     
         11 . A system for simulating annealing to a biological sequence, comprising:
 one or more network computers having stored therein data; and   a host computer having stored therein a biological sequence, the host computer connected to the one or more network computers via a communications network, the host computer configured to identify data in the one or more network computers as relevant data that is relevant to the biological sequence, to perform one of identifying references to the data in the one or more network computers and generating references to the data in the one or more network computer, said references being at least one of a pointer and an address indicating a location of the data associate the relevant data with a segment of the biological sequence, and rank the relevant data based on predetermined criteria applied to functions of the associated segment of the biological sequence to determine a level of affinity of the relevant data with the segment of the biological sequence.   
     
     
         12 . The system of  claim 11 , wherein the host computer is configured to search the network for uniform resource locators (URLs) pointing to the data stored in the one or more network computers, to associate the URLs with the data. 
     
     
         13 . The system of  claim 11 , wherein the host computer is configured to associate the relevant data with one or more probe sequences, the one or more probe sequences corresponding to one or more respective segments of the biological sequence. 
     
     
         14 . The system of  claim 13 , wherein the host computer is configured to competitively rank the one or more probe sequences corresponding to a same segment of the biological sequence, such that a probe sequence having a higher ranking has a higher level of affinity to the segment of the biological sequence than a probe sequence having a lower ranking. 
     
     
         15 . The system of  claim 13 , wherein the host computer is configured to rank the one or more probe sequences based on a correspondence between the one or more probe sequences and the segment of the biological sequence, and
 the host computer is configured to further rank the one or more probe sequences based on at least one of an importance of a source of data associated with the one or more probe sequences, a popularity of the data associated with the one or more probe sequences, and a historical applicability of the data associated with the one or more probe sequences to the segment of the biological sequence.   
     
     
         16 . The system of  claim 15 , wherein the data includes an analysis tool relevant to the segment of the biological sequence,
 the importance of the source of data associated with the one or more probe sequences is based on at least one of a source of the analysis tool and a type of analysis performed by the analysis tool,   a popularity of data associated with the one or more probe sequences is based on a frequency of use of the analysis tool, and   a historical applicability of data associated with the one or more probe sequences is based on a frequency with which an analysis tool has been used to analyze the segment of the biological sequence.   
     
     
         17 . The system of  claim 15 , wherein the data includes a document relevant to the segment of the biological sequence,
 the importance of the source of data associated with the one or more probe sequences is based on at least one of a number of citations of an author of the document and an organization with which the author of the document is associated,   a popularity of data associated with the one or more probe sequences is based on at least one of a number of citations to the document, and   a historical applicability of data associated with the one or more probe sequences is based on a frequency with which the document has been cited in association with the segment of the biological sequence.   
     
     
         18 . The system of  claim 11 , further comprising a display,
 wherein the host computer is configured to display a graphical representation of the segment of the biological sequence on the display and a graphical representation of the level of affinity of relevant data to the segment of the biological sequence on the display by adjusting a physical distance of a graphical representation of the relevant data from the graphical representation of the segment based on the level of affinity of the reference.   
     
     
         19 . The system of  claim 11 , wherein the host computer is further configured to associate the relevant data with a first probe sequence, simulate annealing of the first probe sequence with the segment of the biological sequence based on the determined level of affinity of the relevant data with the segment of the biological sequence, and simulate annealing of a second probe sequence with the first probe sequence based on a determined level of affinity of the second probe sequence with the first probe sequence. 
     
     
         20 . A computer program product for simulating annealing to a biological sequence, comprising:
 a processor; and   a non-transitory computer readable medium having stored thereon code to perform a method, comprising:   identifying, by the processor, references to data in a network as relevant references that are relevant to a biological sequence, said references being at least one of a pointer and an address indicating a location of data or providing information regarding the data;   associating, by the processor, the relevant references with a segment of the biological sequence; and   ranking, by the processor, the relevant references based on predetermined criteria to determine a level of affinity of the relevant references with the segment of the biological sequence.   
     
     
         21 . The computer program product of  claim 20 , wherein the method comprises the relevant references with one or more probe sequences, the one or more probe sequences corresponding to one or more respective segments of the biological sequence; and
 the host computer is configured to competitively rank the one or more probe sequences corresponding to a same segment of the biological sequence, such that a probe sequence having a higher ranking has a higher level of affinity to the segment of the biological sequence than a probe sequence having a lower ranking.   
     
     
         22 . The computer program product of  claim 20 , wherein ranking the relevant references includes ranking the one or more probe sequences based on a correspondence between the one or more probe sequences and the segment of the biological sequence, and
 ranking the one or more probe sequences further includes ranking the one or more probe sequences based on at least one of an importance of a source of data associated with the one or more probe sequences, a popularity of the data associated with the one or more probe sequences, and a historical applicability of the data associated with the one or more probe sequences to the segment of the biological sequence.   
     
     
         23 . The computer program product of  claim 20  wherein the data includes at least one of a document, an analysis tool, and biographical information of a person,
 determining an importance of a source of each reference includes at least one of determining a number of citations of an author of the document, determining an organization to which an author of the document belongs, and determining a type of analysis performed by the analysis tool, 
 determining a popularity of each reference includes at least one of determining a number of citations of the document and a frequency of use of the analysis tool, and 
 determining a historical applicability of each reference to the segment includes at least one of determining a frequency with which the document has been cited in association with the segment of the biological sequence and determining a frequency with which the analysis tool has been used to analyze the segment. 
 
     
     
         24 . The computer program product of  claim 20 , wherein the references correspond to a same segment of the biological sequence, the method further comprising:
 determining a level of affinity of the relevant references with the segment of the biological sequence includes competitively comparing the relevant references such that a reference having a higher ranking is assigned a higher level of affinity than a reference having a lower ranking.   
     
     
         25 . The computer program product of  claim 20 , the method further comprising:
 displaying a graphical representation of the segment of the biological sequence, and displaying a graphical representation of the level of affinity of each reference to the segment of the biological sequence on the display by adjusting a physical distance of a graphical representation of the reference from the graphical representation of the segment based on the level of affinity of the reference.