US 12,087,403 B2
DNA alignment using a hierarchical inverted index table
Michael B. Doerr, Hampton Falls, NH (US); Jan D. Garmany, Austin, TX (US); Stephen V. Wood, Hillsboro, OR (US); Daemon G. Anastas, Portland, OR (US); and Martin A. Hunt, Austin, TX (US)
Assigned to Coherent Logix, Incorporated, Austin, TX (US)
Filed by COHERENT LOGIX, INCORPORATED, Austin, TX (US)
Filed on Feb. 24, 2023, as Appl. No. 18/114,065.
Application 18/114,065 is a continuation of application No. 15/331,239, filed on Oct. 21, 2016, granted, now 11,594,301.
Claims priority of provisional application 62/244,541, filed on Oct. 21, 2015.
Prior Publication US 2024/0203527 A1, Jun. 20, 2024
Int. Cl. G16B 30/10 (2019.01); G06F 16/22 (2019.01); G06F 16/31 (2019.01); G16B 30/00 (2019.01); G16B 50/00 (2019.01); G16B 50/30 (2019.01)
CPC G16B 30/10 (2019.02) [G06F 16/2228 (2019.01); G06F 16/319 (2019.01); G16B 30/00 (2019.02); G16B 50/00 (2019.02); G16B 50/30 (2019.02)] 20 Claims
OG exemplary drawing
 
1. A multiprocessor array (MPA) comprising interspersed processors and communication elements coupled to at least one non-transitory computer-readable memory medium, wherein the at least one non-transitory computer-readable memory medium comprises program instructions executable by the MPA to:
determine a length and a type of an indel in a search sequence using an anchor position in the search sequence, wherein the search sequence is matched to reference data at a match location;
determine a starting position of the indel, wherein, in determining the starting position of the indel, the program instructions are executable to cause the MPA to:
compute a first running error sum between the search sequence and the reference data matched at the match location; and
compute a second running error sum between the search sequence and the reference data matched at an offset from the match location, wherein the offset is based on the type and length of the indel;
determine the starting position of the indel to correspond to a minimum of the second running error sum subtracted from the first running error sum; and
store the length, size, and starting position of the indel in the non-transitory computer-readable memory medium.