HMMCAS – Identifying Cas Genes and Proteins

HMMCAS

:: DESCRIPTION

HMMCAS is a program to identify Cas proteins in archaea and bacteria proteome. You can also use this web tool to find Cas proteins in your interested proteome such as giant virus.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Chai G, Yu M, Jiang L, Duan Y, Huang J.
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1313-1315. doi: 10.1109/TCBB.2017.2665542. Epub 2017 Feb 7. PMID: 28186905.

Cas-Designer 2.4 – A Bulge-allowed quick guide-RNA Designer for CRISPR/Cas derived RGENs.

Cas-Designer 2.4

:: DESCRIPTION

Cas-Designer provides all possible RGEN targets in the given input sequence (e.g. exon), with the useful information including potential off-target numbers within 2nt mismatches and optional 3nt bulge via Cas-OFFinder, and out-of-frame scores via Microhomology-predictor.

::DEVELOPER

Genome Engineering Lab. Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX

:: DOWNLOAD

Cas-Designer

:: MORE INFORMATION

Citation:

Cas-Designer: A web-based tool for choice of CRISPR-Cas9 target sites.
Park J, Bae S, Kim JS.
Bioinformatics. 2015 Sep 10. pii: btv537.

Off-Spotter 0.2.2 – very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

Off-Spotter 0.2.2

:: DESCRIPTION

Off-Spotteris a tool that when presented with a candidate gRNA and a PAM, quickly and exhaustively identifies all genomic sites that are identical or nearly-identical to the gRNA and also satisfy the PAM constraint.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

Off-Spotter

:: MORE INFORMATION

Citation:

“Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs“,
Venetia Pliatsika and Isidore Rigoutsos.
Biol. Direct. 2015;10 :4. doi: 10.1186/s13062-015-0035-z.

CAS 1.8 – Chromosome Aberration Simulator

CAS 1.8

:: DESCRIPTION

CAS is a software for simulating radiogenic aberrations in detail.

::DEVELOPER

Computational Radiation Cytogenetics (CRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX

:: DOWNLOAD

CAS

:: MORE INFORMATION

Citation

Computer simulation of data on chromosome aberrations produced by X rays or alpha particles and detected by fluorescence in situ hybridization.
Chen AM, Lucas JN, Simpson PJ, Griffin CS, Savage JR, Brenner DJ, Hlatky LR, Sachs RK.
Radiat Res. 1997 Nov;148(5 Suppl):S93-101.