Abstract: The invention relates to a tandem mass spectrometer comprising an ionization source that can produce ions; a mass analyzer comprising an ion trap arranged in such a way as to receive ions from the ion source and a detector that can detect ions leaving the ion trap according to the mass to charge (m/z) ratio thereof; ion activation means for activating ions that can fragment at least some of the ions trapped in the ion trap; and coupling means arranged between the ion trap and said ion activation means. According to the invention, the ion activation means consists of a glow discharge lamp that can generate a light beam oriented towards the ion trap, said light beam being electromagnetic radiation in the vacuum ultraviolet wavelength range with photon energies of between 8 eV and 41 eV in such a way as to fragment at least some of the ions trapped in the ion trap.

Abstract: The invention relates to a tandem mass spectrometer comprising an ionization source that can produce ions; a mass analyser comprising an ion trap arranged in such a way as to receive ions from the ion source and a detector that can detect ions leaving the ion trap according to the mass to charge (m/z) ratio thereof; ion activation means for activating ions that can fragment at least some of the ions trapped in the ion trap; and coupling means arranged between the ion trap and said ion activation means. According to the invention, the ion activation means consists of a glow discharge lamp that can generate a light beam oriented towards the ion trap, said light beam being electromagnetic radiation in the vacuum ultraviolet wavelength range with photon energies of between 8 eV and 41 eV in such a way as to fragment at least some of the ions trapped in the ion trap.

Abstract: The invention relates to a tandem mass spectrometer comprising an ionisation source (1) that can produce ions; a mass analyser comprising an ion trap (2) arranged in such a way as to receive ions from the ion source and detection means that can detect ions leaving the ion trap according to the mass m to load z (m/z) ratio thereof; ion activation means for activating ions that can fragment at least some of the ions trapped in the ion trap; and coupling means arranged between the ion trap and said ion activation means. According to the invention, the ion activation means consist of a glow discharge lamp (4) that can generate a light beam oriented towards the ion trap (2), said light beam being electromagnetic radiation in the vacuum ultraviolet wavelength range with photon energies of between 8 eV and 41 eV in such a way as to fragment at least some of the ions trapped in the ion trap (2).

Abstract: Positional Hashing, a novel method for detecting similarities between texts such as DNA sequences, amino acid sequences, and texts in natural language is disclosed. The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes. Positional Hashing is carried out by breaking the sequence comparison problem along its natural structure, solving the subproblems independently, and then collating the solutions into an overall result. The decomposition of the problem into subproblems enables parallelization, whereby a large number of nodes in a computer cluster or a computer farm are concurrently employed on solving the problem without incurring the quadratic time performance penalty characteristic of prior art.

Abstract: A method for assembling nucleic acid sequence fragments is disclosed. The fragments are assembled using information about their relative position inferred by comparison of the fragments against a known sequence of a related nucleic acid (FIG. 3). Additionally, the method localizes fragments to bacterial artificial chromosomes (FIG. 1) and determines relative position of bacterial artificial chromosomes using sequence comparison information (FIG. 6). The method utilizes the information about relative orientation, mutual distance, fragment localization to bacterial artificial chromosomes, and relative position of bacterial artificial chromosomes to constrain the assembly process (FIG. 5), thus resulting in a more accurate assembly requiring fewer sequencing reactions.

Abstract: A method is disclosed for requesting genomics services from a service provider over the Internet and providing genomics services to a client over the Internet. The client provides biological samples and identifies genome sequences of interest. The service provider obtains the biological samples and genome sequences, provides microarrays containing the identified genome sequences, and applies the biological samples to the microarrays. The client receives the results of the analysis over the Internet. The genomics services provided include genotyping, gene expression, and proteomics. The Client is able over the Internet to obtain the current status of the samples and the experiments and to modify the requested experiments based, for example, on the analysis of previously obtained results.

Abstract: A method is disclosed for requesting genomics services from a service provider over the Internet and providing genomics services to a client over the Internet. The client provides biological samples and identifies genome sequences of interest. The service provider obtains the biological samples and genome sequences, provides microarrays containing the identified genome sequences, and applies the biological samples to the microarrays. The client receives the results of the analysis over the Internet. The genomics services provided include genotyping, gene expression, and proteomics. The Client is able over the Internet to obtain the current status of the samples and the experiments and to modify the requested experiments based, for example, on the analysis of previously obtained results.

Abstract: Positional Hashing, a novel method for detecting similarities between texts such as DNA sequences, amino acid sequences, and texts in natural language is disclosed. The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes. Positional Hashing is carried out by breaking the sequence comparison problem along its natural structure, solving the subproblems independently, and then collating the solutions into an overall result. The decomposition of the problem into subproblems enables parallelization, whereby a large number of nodes in a computer cluster or a computer farm are concurrently employed on solving the problem without incurring the quadratic time performance penalty characteristic of prior art.

Abstract: A method for assembling nucleic acid sequence fragments is disclosed. The fragments are assembled using information about their relative position inferred by comparison of the fragments against a known sequence of a related nucleic acid (FIG. 3). Additionally, the method localizes fragments to bacterial artificial chromosomes (FIG. 1) and determines relative position of bacterial artificial chromosomes using sequence comparison information (FIG. 6). The method utilizes the information about relative orientation, mutual distance, fragment localization to bacterial artificial chromosomes, and relative position of bacterial artificial chromosomes to constrain the assembly process (FIG. 5), thus resulting in a more accurate assembly requiring fewer sequencing reactions.

Abstract: Methods are disclosed for the comparison of nucleic acid sequences. Data is generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated is manipulated simultaneously with respect to both (i) matching between oligomers and (ii) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.