Methods and systems for crispr-cas protein pam identification
AssigneeAlia Therapeutics Srl
InventorsAnna CERESETO, Nicola SEGATA, Matteo CICIANI, Antonio CASINI
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Abstract
The disclosure provides methods for predicting protospacer adjacent motif (PAM) sequences recognized by CRISPR-Cas proteins, libraries of CRISPR-Cas proteins having predicted PAM sequences, and uses thereof.
Claims72
A method for predicting a protospacer adjacent motif (PAM) sequence recognized by one or more CRISPR-Cas proteins in a CRISPR-Cas protein cluster, comprising:
- a) mapping spacer sequences of one or more CRISPR arrays corresponding to one or more CRISPR-Cas proteins of the CRISPR-Cas protein cluster to a set of viral genome sequences to identify putative protospacer sequences in the viral genomes and their flanking upstream and downstream sequences in the viral genomes, wherein:
- i) mapping the spacer sequences to the viral genomes comprises aligning the spacer sequences to the viral genome sequences;
- and
- ii) the CRISPR-Cas protein cluster comprises a set of CRISPR-Cas protein sequences clustered by sequence identity;
- b) for each spacer sequence mapped to one or more viral genome sequences, aligning the putative protospacer sequences and their flanking upstream and downstream viral genome sequences to generate a set of aligned putative protospacer and flanking sequences for each mapped spacer sequence;
- and
- c) predicting a PAM sequence recognized by one or more CRISPR-Cas proteins in the cluster from the sets of aligned putative protospacer and flanking sequences.
A computer-implemented method for predicting a protospacer adjacent motif (PAM) sequence recognized by one or more CRISPR-Cas proteins in a CRISPR-Cas protein cluster, the method comprising executing, in a computer system having one or more processors coupled to a memory storing one or more computer readable instructions for execution by the one or more processors, the one or more computer readable instructions comprising instructions for:
- a) mapping spacer sequences of one or more CRISPR arrays corresponding to one or more CRISPR-Cas proteins of the CRISPR-Cas protein cluster to a set of viral genome sequences to identify putative protospacer sequences in the viral genomes and their flanking upstream and downstream sequences in the viral genomes, wherein:
- i) mapping the spacer sequences to the viral genomes comprises aligning the spacer sequences to the viral genome sequences;
- and
- ii) the CRISPR-Cas protein cluster comprises a set of CRISPR-Cas protein sequences clustered by sequence identity;
- b) for each spacer sequence mapped to putative protospacer sequences, aligning the protospacer sequences and their flanking upstream and downstream viral genome sequences to generate a set of aligned putative protospacer and flanking sequences for each mapped spacer sequence;
- and
- c) predicting a PAM sequence recognized by one or more CRISPR-Cas proteins in the cluster from the sets of aligned putative protospacer and flanking sequences.
Dependencies are inferred from the claim text.