bioinformatics methods Search Results


bioinformatics method miranda  (Applied Bioinformatics)
90
Applied Bioinformatics bioinformatics method miranda
Bioinformatics Method Miranda, supplied by Applied Bioinformatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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methods for bioinformatic discovery of class 2 crispr-cas systems  (Broad Institute Inc)
90
Broad Institute Inc methods for bioinformatic discovery of class 2 crispr-cas systems
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Methods For Bioinformatic Discovery Of Class 2 Crispr Cas Systems, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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introduction to mathematical methods in bioinformatics (universitext)  (Verlag GmbH)
90
Verlag GmbH introduction to mathematical methods in bioinformatics (universitext)
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Introduction To Mathematical Methods In Bioinformatics (Universitext), supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatics methods  (Federation of European Neuroscience Societies)
90
Federation of European Neuroscience Societies bioinformatics methods
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatics Methods, supplied by Federation of European Neuroscience Societies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatic analyses and high-throughput sequencing methods  (Wulff labs)
90
Wulff labs bioinformatic analyses and high-throughput sequencing methods
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatic Analyses And High Throughput Sequencing Methods, supplied by Wulff labs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatics methods  (Viome Inc)
90
Viome Inc bioinformatics methods
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatics Methods, supplied by Viome Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatic method alamut  (Interactive Biosoftware)
90
Interactive Biosoftware bioinformatic method alamut
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatic Method Alamut, supplied by Interactive Biosoftware, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ingenious bioinformatics methods  (Schmid GmbH)
90
Schmid GmbH ingenious bioinformatics methods
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Ingenious Bioinformatics Methods, supplied by Schmid GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatic methods  (Amcare Inc)
90
Amcare Inc bioinformatic methods
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatic Methods, supplied by Amcare Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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statistical methods in bioinformatics an introduction  (Verlag GmbH)
90
Verlag GmbH statistical methods in bioinformatics an introduction
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Statistical Methods In Bioinformatics An Introduction, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hilic-esi-ms method  (Applied Bioinformatics)
90
Applied Bioinformatics hilic-esi-ms method
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Hilic Esi Ms Method, supplied by Applied Bioinformatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioinformatic methods 1  (Coursera Inc)
90
Coursera Inc bioinformatic methods 1
a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established <t>bioinformatic</t> pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.
Bioinformatic Methods 1, supplied by Coursera Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established bioinformatic pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.

Journal: Nature cell biology

Article Title: RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering

doi: 10.1038/s41556-019-0454-7

Figure Lengend Snippet: a, Cas proteins, including RCas, are discovered in metagenomic sequencing of bacteria and archaea using an established bioinformatic pipeline. Starting with a CRISPR array search seed, nearby putative Cas effectors are filtered on the basis of various criteria, including co-correlation with CRISPR arrays, size, and predicted protein domains. After grouping based on homology, distinct groups of effectors are selected for experimental validation follow-up. Researchers deduce the targeting substrate and mechanism through biochemical incubation of substrate nucleic acids with purified CRISPR ribonucleoprotein complexes and by observing resultant cleavage and binding. Genetic interrogation of targeting rules can be achieved through a spacer depletion screen assay consisting of a CRISPR library with spacers targeting an antibiotic resistance gene. Bacterial co-transformation via plasmids containing (i) the spacer library and Cas effector and (ii) the antibiotic resistance gene, followed by computational analysis of depleted spacers in the sequenced surviving population, will yield any targeting-dependent sequence requirements vis-à-vis the spacer. b, Type II and VI systems, encapsulating Cas9 and Cas13, respectively, represent the most commonly used RCas systems. Cas9 binds to a tracrRNA and crRNA (often combined into a single sgRNA) to target RNA. Depending on the Cas9 variant, a PAMmer oligonucleotide comprising a PAM sequence may be required for RNA binding10 and an additional domain (such as PIN domain endonuclease) may be required for RNA cleavage47. Cas13 binds to a crRNA for effective RNA targeting and subsequent indiscriminate cleavage. c, Prokaryotic Argonaute (pAgo) systems resemble CRISPR-Cas systems in their ability to target nucleic acids with a programmable guide. They exist as part of a broader RNA-targeting ecosystem that includes antisense oligonucleotides (ASOs), RNA interference (RNAi), CRISPR-Cas-inspired RNA targeting systems (CIRTS), viral coat proteins (VCPs), zinc fingers, Pumilio and FBF homology proteins (PUFs), and pentatricopeptide repeat proteins (PPRs), among others.

Article Snippet: Competing interests A.A.S. declares inventorship on the following published patents, applied for by the Broad Institute of MIT and Harvard and the Massachusetts Institute of Technology: WO2018035250A1 on methods for bioinformatic discovery of class 2 CRISPR-Cas systems; WO2017070605 on systems, methods, and compositions for targeting nucleic acids with type VI-B CRISPR-Cas systems.

Techniques: Sequencing, Bacteria, CRISPR, Biomarker Discovery, Incubation, Purification, Binding Assay, Transformation Assay, Variant Assay, Zinc-Fingers