Casboundary v1.0.1 – Automated Definition of integral CRISPR/Cas Cassettes

Casboundary v1.0.1

:: DESCRIPTION

Casboundary is the first method able to automatically define CRISPR cassette boundaries. In addition, it contains a Cas type predictive model used to assign each gene located in the region defined by a cassette’s boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules.

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Casboundary

:: MORE INFORMATION

Citation

Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, Carvalho ACPLF, Backofen R.
Casboundary: automated definition of integral Cas cassettes.
Bioinformatics. 2021 Jun 16;37(10):1352-1359. doi: 10.1093/bioinformatics/btaa984. PMID: 33226067; PMCID: PMC8208735.

CRISPRloci – Annotation of CRISPR-Cas Systems

CRISPRloci

:: DESCRIPTION

CRISPRloci provides an automated and comprehensive in silico characterization of CRISPR-Cas system on bacterial and archaeal genomes. It is a full suite for CRISPR locus characteriztion that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation and subtype classification.

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CRISPRloci

:: MORE INFORMATION

Citation

Alkhnbashi OS, Mitrofanov A, Bonidia R, Raden M, Tran VD, Eggenhofer F, Shah SA, Öztürk E, Padilha VA, Sanches DS, de Carvalho ACPLF, Backofen R.
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems.
Nucleic Acids Res. 2021 Jul 2;49(W1):W125-W130. doi: 10.1093/nar/gkab456. PMID: 34133710; PMCID: PMC8265192.

CGD – Comprehensive Guide Designer for CRISPR-Cas systems

CGD

:: DESCRIPTION

CGD is a Comprehensive Guide Designer for four different CRISPR systems, which utilizes the machine learning algorithm, Elastic Net Logistic Regression (ENLOR), to autonomously generalize the models.

The CGD is a predictive regression models that predict efficient gRNAs for CRISPRi, CRISPRa, Cas9, Cas12a in a comprehensive manner.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Menon AV, Sohn JI, Nam JW.
CGD: Comprehensive guide designer for CRISPR-Cas systems.
Comput Struct Biotechnol J. 2020 Mar 25;18:814-820. doi: 10.1016/j.csbj.2020.03.020. PMID: 32308928; PMCID: PMC7152703.