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DeepCpf1
Predicts AsCpf1 (Cpf1 from Acidaminococcus sp. BV3L6) activity based on target sequence composition. DeepCpf1 is a web application that performs with a 34-bp target sequence and produces a regression score that correlates with AsCpf1 activity. It learns informative representations of target sequences relevant to AsCpf1 activity profiles. It works in two steps: (1) model selection and pre-training of the entire architecture; and (2) fine-tuning with endogenous target data considering an additional chromatin accessibility input.
CRISPRFinder
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An interface to extract with precision and to further analyse clustered regularly interspaced short palindromic repeats (CRISPRs) from genomic sequences. Four main advantages may be cited: (i) short CRISPR-like structures are detected, they are labelled questionable but may be of great interest if later confirmed; (ii) conserved regions are accurately defined to single base pair resolution; (iii) summary files may be uploaded (CRISPR properties summary and spacers file in Fasta format) and (iv) flanking sequences or spacers can be easily extracted and blasted against different databases.
CRISPRcompar
Proposes a set of bioinformatic tools assisting biologists in the development and the setting up of a CRISPR genotyping scheme. In the pre-processing phase, the comparison of CRISPRs is mandatory and may be fulfilled using the CRISPRcomparison tool, which helps in selecting the most appropriate CRISPR loci and associated primers for the PCR amplification. CRISPRcomparison allows the identification of families of strains that share a CRISPR, inside species with high genetic diversity or the identification of homologous CRISPRs within species containing multiple CRISPR loci. In the post-processing phase, the CRISPRtionary program is very interesting since it allows the user to easily compare multiple alleles of a CRISPR locus investigated in a collection of strains and to obtain pre-calculated files that may be directly used in clustering analysis.
PRAP / Prokaryotic Repeats Annotation Program
Automates the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared with the major existing repeat finding tools, PRAP exhibits competitive or better results. The results are consistent with manually curated and experimental data. Repeats can be identified and grouped into families to define their relevant types. The final output is parsed into the European Molecular Biology Laboratory (EMBL)/GenBank feature table format for reading and displaying in Artemis, where it can be combined or compared with other genome data. It is currently the most complete repeat finder for prokaryotes and is a valuable tool for genome annotation.
Green Listed
Designs custom Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screens targeting sets of genes defined by the user. Green Listed is a web-based tool facilitating the rapid design of custom CRISPR screens. It is used to mine publicly available source lists/reference libraries of gRNAs to design custom libraries targeting genes specified by the user, such as all kinases or all genes up-regulated in an RNAseq experiment. Green Listed enables researchers to rapidly design custom CRISPR screens against a selected list of genes.
CRISPRTarget
Predicts the most likely targets of CRISPR RNAs. This can be used to discover targets in newly sequenced genomic or metagenomic data. The inputs into CRISPRTarget are predicted CRISPR arrays or spacer sequences. The output provided is either visual in HTML format, but can also be saved as text and opened in a spreadsheet. The target sequence is typically displayed as an R-loop, depicting a specified part of the crRNA, as well as both the target and non-target strand of the double-stranded target DNA. The target sequence R-loop can be fully reverse complemented, when users suspect that the direction of transcription of the CRISPR array starts from the downstream end instead.
CRISPRDetect
A web-based and command line tool, that enables accurate identification of CRISPR arrays in genomes, their direction, repeat spacer boundaries, substitutions, insertions or deletions in repeats and spacers and lists cas genes that are annotated in the genome. This data is combined into a searchable database, CRISPRBank, currently version 1.0. Spacer outputs from CRISPRDetect can then be directly used to search for targets in viral and other sequence databases using the linked tool, CRISPRTarget. CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.
CRISPRone
Provides annotation of CRISPR—Cas systems including (i) CRISPR arrays of repeat-spacer units, and cas genes, (ii) type (and subtype) of predicted system(s) and (iii) anti-repeats (part of tracrRNA genes in type II CRISPR–Cas systems). The CRISPRone website also provides online prediction of CRISPR–Cas systems given genomic sequences, using a pipeline with integrated checking of false-CRISPRs. It can be used to submit sequences to the server for prediction, look up pre-calculated CRISPR-Cas systems or check out mock CRISPRs (elements that superficially reassemble CRISPRs).
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