ABS-Scan – Webserver for Insilico Binding site Alanine Scanning Mutagenesis

ABS-Scan

:: DESCRIPTION

ABS-Scan performs alanaine scanning mutagenesis for a given protein-ligand complex.

::DEVELOPER

Chandra Lab, Dept. of Biochemistry.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.
Anand P, Nagarajan D, Mukherjee S, Chandra N.
Version 2. F1000Res. 2014 Sep 9 [revised 2014 Dec 1];3:214. doi: 10.12688/f1000research.5165.2. eCollection 2014.

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5 – Primer Design and Sequence Analysis for High-throughput Scanning Mutagenesis

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5

:: DESCRIPTION

AAscan, PCRdesign and MutantChecker is a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.

AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning

::DEVELOPER

Laboratory of Biomolecular Research (LBR)

:: SCREENSHOTS

aascan

MutantChecker

PCRCloning

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AAScan, MutantCheckerPCR Cloning

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 30;8(10):e78878. doi: 10.1371/journal.pone.0078878. eCollection 2013.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
Sun D1, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB.

MH-ESS 1.21 – Bayesian Analysis of Transposon Mutagenesis Data

MH-ESS 1.21

:: DESCRIPTION

MH-ESS is a python implementation of the Bayesian analysis method. It utilizes read information obtained from sequencing libraries of transposon mutants, to determine the essentiality of genes. Using a Bayesian framework, essentiality is modeled through the Extreme Value (Gumbel) distribution, which characterizes the maximum run of non-insertions (i.e. number of consecutive TA sites lacking insertion in a row). Genes with significantly larger runs of non-insertion thant statistically expected have a higher likelihood of essentiality. A Metropolis-Hastings sampling procedure is utilized to sample from conditional densities of essentiality for all genes, and posterior estimates of the probability of being essential are estimated for all genes.

::DEVELOPER

Sacchettini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python
  • Scipy
  • Numpy

:: DOWNLOAD

 MH-ESS

:: MORE INFORMATION

Citation

Michael DeJesus; Yanjia J. Zhang; Christopher M. Sassetti; Eric J. Rubin; James C. Sacchettini; Thomas R. Ioerger
Bayesian Analysis of Gene Essentiality based on Sequencing of Transposon Insertion Libraries
Bioinformatics (2013) 29 (6): 695-703.

MuSi – Analysis of Gene Libraries Generated by Dodon-directed Mutagenesis

MuSi

:: DESCRIPTION

MuSi (Mutation Site) was designed to analyze (aligned) gene libraries, in particular in case that codon directed mutagenesis was applied to them. The program generates several tables providing information about trinucleotide characteristics, deletions, substitutions and amino acids distributions.

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

MuSi

:: REQUIREMENTS

  • Linux / Mac OS X / Windows
  • Java

:: DOWNLOAD

 MuSi

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Mar;40(6):e47. doi: 10.1093/nar/gkr1294. Epub 2011 Dec 30.
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.
Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM.

SiteFind 4.0 – A Site-directed Mutagenesis Software Tool

SiteFind 4.0

:: DESCRIPTION

SiteFind is a molecular biology tool that enables a scientist performing site-directed mutagenesis to simultaneously introduce a restriction site as a maker for successful mutagenesis.

::DEVELOPER

Paul Evans @ the Sealy Center for Cancer Cell Biology.

:: SCREENSHOTS

SiteFind

:: REQUIREMENTS

  • Linux / MacOSX / WIndows
  • Java

:: DOWNLOAD

  SiteFind

:: MORE INFORMATION

Citation

BMC Mol Biol. 2005 Dec 1;6:22.
SiteFind: a software tool for introducing a restriction site as a marker for successful site-directed mutagenesis.
Evans PM, Liu C.