# US 2021/0174902 A1 · Recombinase discovery > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2021/0174902 A1 - Document ID: US20210174902A1 - Status: Published application - Kind: A1 - Application number: 17/117,921 - Filed: 2020-12-10 - Published: 2021-06-10 - Earliest claimed: 2019-12-10 - Assignees: Homodeus, Inc. - Applicants: Homodeus, Inc. - Inventors: Harry Kemble; Spencer Glantz; Jonathan M. Rothberg - Web page: https://patentgrep.com/patent/US20210174902A1 ## CPC - G16B 30/10: Sequence alignment; Homology search - G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding - C12N 15/85: for animal cells - C12N 2320/10: in screening processes - C12N 2800/30: Vector systems comprising sequences for excision in presence of a recombinase, e.g. loxP or FRT - C12N 2800/80: Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) ## Abstract The present disclosure provides methods, compositions, kits, and systems for identifying recombinases and cognate site-specific recombinase recognition sites as well as method for using the identified recombinase/recognition site pairs. ## Claims ### Claim 1 A method comprising: mining from a protein database putative recombinase sequences based on conserved recombinase domain architecture or other measure of homology to known recombinases; linking the putative recombinase sequences to prokaryotic genomic sequences containing their corresponding coding sequences; scanning those genomic sequences to identify prophage sequences containing the coding sequences; aligning the prophage sequences and their boundary-flanking sequences with homologous genomic sequences, optionally, from the same genus to produce sequence alignments; and automatically solving for putative cognate recombinase recognition sites by detecting overlapping sequences in the sequence alignments, thereby producing a solved recombinase list. ### Claim 2 (depends on 1) The method of claim 1, wherein the mining is based on a precisely ordered recombinase domain superfamily architecture or other measure of homology to known recombinases. ### Claim 3 (depends on 1) The method of claim 1, wherein the linking includes accessing a database that comprises annotated records of genomes assembled from long-read nucleotide sequences, short-read nucleotide sequences, or a combination of long- and short-read nucleotide sequences, or directly annotated records of long-read nucleotide sequences. ### Claim 4 (depends on 1) The method of claim 1, wherein the linking includes automatically removing uninformative nucleotide sequences from the genomic coding sequences. ### Claim 5 (depends on 1) The method of claim 1, wherein the genomic coding sequences includes at least 2, at least 5, at least 10, at least 25, at least 50, or at least 100 annotated genomic coding sequences. ### Claim 6 (depends on 1) The method of claim 1, wherein the boundary-flanking sequences have a length of at least 20 kilobases. ### Claim 7 (depends on 1) The method of claim 1, wherein the automatically solving includes defining multiple putative cognate recombinase recognition sites for a single recombinase. ### Claim 8 (depends on 1) The method of claim 1, wherein the automatically solving includes implementation of an algorithm that includes a measure of confidence in each predicted recombinase recognition site set, optionally in the form of ambiguity scores. ### Claim 9 (depends on 1) The method of claim 1, further comprising verifying that all putative cognate recombinase recognition sites solved flank a sequence encoding at least one of the putative recombinase sequences. ### Claim 10 (depends on 1) The method of claim 1, wherein the putative recombinase sequences comprise tyrosine and/or serine recombinase sequences, optionally wherein the serine recombinase sequences comprise resolvase and/or integrase sequences. ### Claim 11 (depends on 1) The method of claim 1, further comprising continuously updating the solved recombinase list as the protein database is updated. ### Claim 12 A computer readable medium on which is stored a computer program which, when implemented by a computer processor, causes the processor to: mine from a protein database putative recombinase sequences based on conserved recombinase domain architecture or other measure of homology to known recombinases; link the putative recombinase sequences to prokaryotic genomic sequences containing their corresponding coding sequences; scan those genomic sequences to identify prophage sequences containing the coding sequences; align the prophage sequences and their boundary-flanking sequences with homologous genomic sequences from the same genus to produce sequence alignments; and solve for putative cognate recombinase recognition sites by detecting overlapping sequences in the sequence alignments. ### Claim 13 (depends on 12) The computer readable medium of claim 12, wherein the mining is based on a precisely ordered recombinase domain superfamily architecture or other measure of homology to known recombinases. ### Claim 14 (depends on 12) The computer readable medium of claim 12, wherein the linking includes accessing a database that comprises annotated records of genomes assembled from long-read nucleotide sequences, short-read nucleotide sequences, or a combination of long- and short-read nucleotide sequences, or directly annotated records of long-read nucleotide sequences. ### Claim 15 (depends on 12) The computer readable medium of claim 12, wherein the linking includes automatically removing uninformative nucleotide sequences from the genomic coding sequences. ### Claim 16 (depends on 12) The computer readable medium of claim 12, wherein the solving includes (i) defining multiple putative cognate recombinase recognition sites for a single recombinase; or (ii) implementation of an algorithm that includes a measure of confidence in each predicted recombinase recognition site set, optionally in the form of ambiguity scores. ### Claim 17 (depends on 12) The computer readable medium of claim 12, further comprising verifying that all putative cognate recombinase recognition sites solved flank a sequence encoding at least one of the putative recombinase sequences. ### Claim 18 (depends on 12) The computer readable medium of claim 12, further comprising continuously updating the solved recombinase list as the protein database is updated. ### Claim 19 A system configured to perform: mining a protein database putative recombinase sequences based on conserved recombinase domain architecture or other measure of homology to known recombinases; linking the putative recombinase sequences to prokaryotic genomic sequences containing their corresponding coding sequences; scanning those genomic sequences to identify prophage sequences containing the coding sequences; aligning the prophage sequences and their boundary-flanking sequences with homologous genomic sequences from the same genus to produce sequence alignments; and solving for putative cognate recombinase recognition sites by detecting overlapping sequences in the sequence alignments. ### Claim 20 (depends on 19) The system of claim 19, wherein the system is a computer system.