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US 2021/0174902 A1Published application
Recombinase discovery
AssigneeHomodeus, Inc.
InventorsHarry Kemble, Spencer Glantz, Jonathan M. Rothberg
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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.
Claims20
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.
3 more elements
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.
3 more elements
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.
3 more elements
Dependencies are inferred from the claim text.