Patent ID: 7822782

Claim:
A computer program product implemented on a computer or stored on a computer readable storage medium for predicting strains of some pathogens from limited sequence data, the computer product comprising: a graphical user interface (GUI) code implemented on the computer or encoded on the computer readable storage medium and operable to carry out all data input-output (I/O) operations, where the GUI code uses a sequence category region of a screen of a display of an implementing computer to allow users to input sequence data in a specified format using a paste option or by reading in files containing the data, where the GUI code uses a database category region of the screen to use default reference sequences or allow users to pre-select specific reference sequence to facilitate sequence comparisons, and where the GUI code uses an output options category region of the screen to allow users to selectively display identifiers of each input sequence and summary/details of matches of characteristic residues for an input query sequence specified by its identifier; a storage code implemented on the computer or encoded on the computer readable storage medium and operable to identify characteristic residues of individual virus sequences or their groups from program supplied external files and to store virus sequence databases in the form of multiple data arrays including information about phylogenetic trees, sequence groups and characteristic residues of these groups, where arrays are in the form tree-like multiple 2-dimensional arrays for efficient referencing and retrieval; a sequence comparison code implemented on the computer or encoded on the computer readable storage medium and operable to compare input pathogen sequences with the stored database sequences on a residue-by-residue basis to produce comparisons corresponding to all pathogens or pathogen strains stored in the database that include some or all of the input pathogen sequences; and an identification code implemented on the computer or encoded on the computer readable storage medium and operable to identify the pathogens or pathogen strains of input pathogen sequences based on the comparisons and subsequent decision making algorithms, where the algorithms identifies the comparison pathogens or pathogen strains that include maximal sequence identify.