Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2001-01-30
2004-08-10
Brusca, John S. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
Reexamination Certificate
active
06775622
ABSTRACT:
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TECHNICAL FIELD
This invention relates to the field of computer systems. More particularly, the present invention relates to a method and system for evaluating and comparing biological sequences using various computer related methods and systems.
BACKGROUND OF THE INVENTION
Computer programs and systems are known for generating and maintaining large databases of biological sequences (e.g., deoxyribonucleic acid (DNA), ribonucleic acid (RNA), amino acid sequences) derived from living organisms. Similarly, computer programs and systems are known for manipulating these databases in various ways to search for genes that can be used for various human testing, drug target identification and therapeutics.
As an illustration, the human genome, the complete, single-copy set of genetic instructions for a human, is being sequenced by many groups using several techniques with different purposes in an ongoing process. The various groups, techniques and purposes result in some fragments of the human genome being represented more than once in the genomic DNA databases. The inflated human genomic DNA database causes two problems addressed here. First, the time required to search the database is directly related to the size of the database. By removing redundancy from the database, the time to perform a search is reduced allowing more searches and more sensitive searches. Second, as searches are performed, the DNA sequences are annotated with the results. These annotations can be valuable and must be applied to all identical sequences in the genomic DNA database. A confounding factor is the dynamic nature of the genomic DNA database, wherein daily new sequences are added, old sequences removed and sequences are modified. For example, assume a sequence named ABC is in the genomic database and is annotated as “XYZ.” This database could be updated tomorrow and the sequence formerly named ABC could then be called DEF. It is desirable to be able to apply the annotation “XYZ” to the sequence DEF.
Remote homologue detection (that is, detection of similarities within some range of similarity, such as <30%, etc.) has been the focus of many sequence similarity identification programs such as the Basic Local Alignment Search Tool (BLAST), hidden Markov models, and others. The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities.
While remote homologue detection will remain a central problem in bioinformatics, a critical technical problem presently exists in the attempt to quickly identify regions of near identity in large sequence databases.
There is a need in the art for a method of efficiently detecting near identities in large DNA databases in such a way as to make feasible a system to keep up with the daily additions that are being made to publicly available sequence databases.
There is a further need for such a system in order to provide solution mechanisms for hitherto unsolved problems such as: 1) removing redundancy from genomic sequence databases, 2) mapping (assembled) expressed sequence tags (ESTs)/sequence tagged sites (STSs)/complementary DNA molecules (cDNAs) onto genomic sequence, 3) assembling ESTs into the cDNAs they were derived from, and 4) searching EST/cDNA databases for alternately spliced cDNAs and single nucleotide polymorphisms (SNPs). An EST is a transcript corresponding to an expressed gene, the defined transcript sequence “tag” being a marker for a gene, which is expressed in a cell, a tissue, or an extract, for example. A SNP is an alteration in a single nucleotide base within a DNA sequence, which differs between individuals.
SUMMARY OF THE INVENTION
The present invention provides a solution to the needs described above through a system and method for detecting near identities in large DNA databases. The system and method disclosed herein make use of an algorithm used to construct and maintain a unique nucleotide database wherein the unique database contains no two DNA sequences such that one is contained in the other. The system and method are applicable to problems such as an all against all comparison of all available genomic sequence data, clustering and assembling ESTs into the cDNAs that generated the ESTs, mapping assembled ESTs onto genomic sequence, mapping cDNAs onto genomic sequences and locating alternately spliced cDNAs.
A system and method are disclosed for finding near identities in a DNA sequence database wherein tag arrays are generated for each of a first and a second database of sequences, and wherein near identities of sequences in the two databases are identified using a comparison model.
A system and method are also disclosed for finding near identities when the first and second databases are both genomic DNA sequence databases; when the first database is a genomic DNA database and the second database is a cDNA sequence database; when the first and second databases are both cDNA databases.
Similarly, a computer program stored on a computer readable medium or carrier wave is disclosed having computer code mechanisms for finding near identities in a DNA sequence database wherein tag arrays are generated for each of a first and a second database of sequences, and wherein near identities of sequences in the two databases are identified using a comparison model.
Also disclosed is a computer program for finding near identities in a DNA sequence database, the computer program having code mechanisms for generating tag arrays for each of a first and a second database of sequences, and wherein near identities of sequences in the two databases are identified using a comparison model.
Brusca John S.
Walker Shelby J.
ZymoGenetics Inc.
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