Amino acid Hilbert mapping
A file is received that includes locus information. The received file is preprocessed, including by selecting a size for a Hilbert curve. File contents are transformed using the Hilbert curve. The transformed file contents are down-sampled. A hashing operation is performed on the down-sampled result.
1 . A system, comprising:
an interface configured to receive a file including locus information;
a processor configured to:
preprocess the received file, including by selecting a size for a Hilbert curve based at least in part on a number of amino acids represented in the file, including by dividing a number of base pairs by three and determining a power of four larger than a result of the dividing;
transform file contents using the Hilbert curve;
down-sample the transformed file contents; and
perform a hashing operation on the down-sampled result; and
make a result of the hashing operation available for at least one of: (1) searching or (2) clustering operations; and
a memory coupled to the processor and configured to provide the processor with instructions.
2 . The system of claim 1 , wherein the file is received in a FASTA format.
3 . The system of claim 1 , wherein the file includes a plurality of base pairs.
4 . The system of claim 1 , wherein the preprocessing further includes, for a first codon included in the file, mapping each letter of the first codon to a bit pattern.
5 . The system of claim 1 , wherein the preprocessing further includes, for a bit pattern, inserting two zero bits between a first half and second half of the bit pattern.
6 . The system of claim 1 , wherein the down-sampling the transformed file contents includes performing a blur operation.
7 . The system of claim 1 , wherein the down-sampling the transformed file contents includes performing an anti-aliasing operation.
8 . The system of claim 1 , wherein the down-sampling the transformed file contents includes performing a resize operation.
9 . The system of claim 1 , wherein performing the hashing operation includes performing locality sensing hashing.
10 . The system of claim 1 , wherein the processor is further configured to determine a cluster associated with the file.
11 . The system of claim 1 , wherein the processor is further configured to generate a signature based at least in part on a located string occurring in a threshold number of other files.
12 . A method, comprising:
receiving a file including locus information;
preprocessing the received file, including by selecting a size for a Hilbert curve based at least in part on a number of amino acids represented in the file, including by dividing a number of base pairs by three and determining a power of four larger than a result of the dividing;
transforming file contents using the Hilbert curve;
down-sampling the transformed file contents;
performing a hashing operation on the down-sampled result; and
making a result of the hashing operation available for at least one of: (1) searching or (2) clustering operations.
13 . The method of claim 12 , wherein the file is received in a FASTA format.
14 . The method of claim 12 , wherein the file includes a plurality of base pairs.
15 . The method of claim 12 , wherein the preprocessing further includes, for a first codon included in the file, mapping each letter of the first codon to a bit pattern.
16 . The method of claim 12 , wherein the preprocessing further includes, for a bit pattern, inserting two zero bits between a first half and second half of the bit pattern.
17 . The method of claim 12 , wherein the down-sampling the transformed file contents includes performing a blur operation.
18 . The method of claim 12 , wherein the down-sampling the transformed file contents includes performing an anti-aliasing operation.
19 . The method of claim 12 , wherein the down-sampling the transformed file contents includes performing a resize operation.
20 . The method of claim 12 , wherein performing the hashing operation includes performing locality sensing hashing.
21 . The method of claim 12 , further comprising determining a cluster associated with the file.
22 . The method of claim 12 , further comprising generating a signature based at least in part on a located string occurring in a threshold number of other files.