Specific identifiers of amino-acid base sequences

• US 7,164,991 B1
• Filed: 08/11/2000
• Issued: 01/16/2007
• Est. Priority Date: 08/11/1999
• Status: Expired due to Fees

• Current Assignee: Institute of Medicinal Molecular Design, Inc.
• Original Assignee: Institute of Medicinal Molecular Design, Inc.
• Inventors: Itai, Akiko, Toyoda, Tetsuro
• Primary Examiner(s): Martinell; James
• Application Number:
  US10/048,479
• Time in Patent Office: 2,349 Days
• Field of Search: 702/19, 702/20
• US Class Current: 702/19
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

In order to assign specific identifiers to amino-acid sequences and base sequences, specific identifiers of sequences are generated from data representing connection order of residues in the sequences by using a conversion function, such as collision intractable hash function or universal one-way hash function, and are assigned to the sequences.

Claims

1. A method of generating an identifier specific to a base sequence or an amino-acid sequence or a segment/segments of a sequence comprising converting data with a conversion function to generate the identifier, wherein the data comprises a representation of connection order of residues in the sequence or the segment/segments of the sequence, and wherein the generated identifier is specific to the sequence and specific to descriptive information related to the sequence other than strings of characters representing the sequence of amino acids or nucleotides, and wherein the identifier is derived from the sequence itself.

2. The method of claim 1, in which the data representing connection order of the residues is transformed to a standard representation which is converted to the identifier, whereby the conversion function generates the same identifier regardless of the initial representation of the same sequence or the same segment/segments of the sequence.

3. The method of claim 1, wherein the conversion function comprises one or more collision-intractable hash functions and/or universal one-way hash functions.

4. The method of claim 1, wherein the conversion function comprises secure hash algorithm (SHA) or SHA1.

5. The method of claim 1, wherein the identifier is appended with one or more characters representing the generation method of the identifiers and/or additional information.

6. The method of claim 1, wherein the identifier has a fixed length.

7. A method of assigning the same identifier to the same sequence and/or to the same segment/segments of the sequence that occurs more than once among data records of one or more databases, comprising converting sequence data for each same sequence and/or to the same segment/segments with the same conversion function by a method of claim 1.

8. A method of generating an identifier of a group including multiple sequences and/or segment/segments of sequences, comprising generating an identifier for each member of the group by the method of claim 1, and generating an identifier specific to combination of the identifiers of the sequences and/or segment/segments of the sequences in the group.

9. A method of judging the identicalness of sequences, segment/segments of sequences, genotypes and/or alleles by comparing identifiers generated by the method of claim 1.

10. A method of searching a data record containing a sequence or segment/segments of a sequence or a genotype or an allele by directly generating an identifier from data representing connection order of residues by a method of claim 1, and by searching for one or more data records in one or more databases using the identifier.

11. The method of claim 1, comprising storing the identifier and/or one or more data records containing the identifier on a storage a device or a recording medium.

12. A storage device or a medium recording a program comprising the method of claim 1, and a device for generating an identifier according to the method of claim 1.

13. A method of generating an identifier of a data record containing a sequence or segment/segments of a sequence, wherein the identifier is generated from both the identifier generated by a method of claim 1 and information related to the sequence or segment/segments of the sequence in the data record, whereby the generated identifier is specific to combination of the sequence or segment/segments of the sequence and information related to the sequence of segment/segments of the sequence in the data record.

14. The method of claim 13 wherein the identifier is specific for a sequence and/or segment/segments of a sequence of a selected genotype or allele.

15. The method of claim 14, wherein the identifier describes a relation among sequences and/or segment/segments of sequences and/or genotypes and/or alleles.

16. The method of claim 14, wherein the identifier describes information related to sequences and/or segment/segments of sequences and/or genotypes and/or alleles.

17. The method of claim 14, wherein the identifier is compared with identifiers generated of one or more data records in one or more databases to identify the occurrence of the same identifier, or a part thereof.

18. The method of claim 14, wherein the identifier describes an association of an identifier with one or more data records in one or more databases.

19. The method of claim 18, wherein the data record does not include data representing connection order of residues in a sequence or segment/segments of the sequence.