METHOD OF ALIGNING STRINGS OF CHARACTERS REPRESENTING GENOMIC DATA AND RELATED HARDWARE DEVICE

• Main Authors: ZENI, Alberto, PIZZATO, Fabio, CRESPI, Matteo, DI TUCCI, Lorenzo, SANTAMBROGIO, Marco Domenico
• Format: Patent
• Language: English; French; German
• Published: 07.06.2023
• Subjects: INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS; PHYSICS

A method of aligning a first string (read) of characters representing genomic data to a second string (contig) of characters representing genomic data, using at least a Finite State Machine having a storage memory, is disclosed. Substantially, data representing at least a first string of characters representing genomic data (read) and at least a second string of characters representing genomic data (contig) are loaded into a storage memory and a first block of characters of the read and a second block of characters of the contig are selected, wherein the two blocks have the same number of characters and are identified respectively by a first index and by a second index pointing to start positions of the two blocks. Then the two blocks of characters are compared and the two indexes are updated at each cycle of the Finite State Machine until all blocks of characters of the read have been compared. It is also disclosed a hardware device, preferably a FPGA, configured for executing the disclosed method.