Tn-seq Explorer 1.5b – Analysis of High-throughput Sequencing data of Transposon Mutant Libraries

Tn-seq Explorer 1.5b

:: DESCRIPTION

Tn-seq Explorer allows users to explore and analyze Tn-seq data for prokaryotic (bacterial or archaeal) genomes.

::DEVELOPER

Sina Solaimanpour ,Computational Microbiology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • JAVA

:: DOWNLOAD

   Tn-seq Explorer

:: MORE INFORMATION

Citation

Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries.
Solaimanpour S, Sarmiento F, Mrázek J.
PLoS One. 2015 May 4;10(5):e0126070. doi: 10.1371/journal.pone.0126070

MuStab – Predicting Mutant Protein Stability Change

MuStab

:: DESCRIPTION

MuStab is designed for predicting protein stability changes upon amino acid substitutions.

::DEVELOPER

MuStab team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 2;11 Suppl 2:S5. doi: 10.1186/1471-2164-11-S2-S5.
Sequence feature-based prediction of protein stability changes upon amino acid substitutions.
Teng S1, Srivastava AK, Wang L.

TSpred – Predict Substitutions that Transform Query Protein Sequence/structure into Temperature-sensitive Mutant

TSpred

:: DESCRIPTION

TSpred attempts to identify a small set of amino acid residues in a query protein that have a high probability of being buried (side-chain accessibilities less than 5%, expressed in terms of residue depth). The server suggests substitutions at these buried positions that are most likely to result in a temperature sensitive (Ts) phenotype.

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Apr 29. [Epub ahead of print]
TSpred: a web server for the rational design of temperature-sensitive mutants.
Tan KP1, Khare S, Varadarajan R, Madhusudhan MS.

MUTANT – MUTation ANnotation Tool

MUTANT

:: DESCRIPTION

The MUTANT tool was implemented as a standalone software that can connect to the Internet to retrieve other related genomic information from ThaiMUT database . To generate the mutation nomenclature, the gene sequences and others information including pseudogene information are retrieved from the online ThaiMUT database where users can locally store such information for future use. To facilitate the mutation annotation, MUTANT can graphically display the human genome gene structure (exon, intron, up/downstream regions, etc.) via querying of a target gene symbol. Once the target area is located, users can annotate the mutation by a simple point and click on the location as well as selecting the type of mutation, e.g., substitution, insertion, deletion and others. MUTANT can also display mutations through a popular web-visualization- interface, named GBrowse as well as offering the listing of annotated mutation results in both nucleotide and amino acid forms. Comparison among different ethnic specific databases can be also be done by using the extensible markup language (XML) exporting feature of MUTANT.

::DEVELOPER

Genome Institute, BIOTEC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MUTANT

:: MORE INFORMATION

Citation

Uttapong Ruangrit, Anunchai Assawamakin, Chumpol Ngamphiw, Bunyarit Uyyanonvara, Sissades Tongsima.
MUTation ANnotation Tool (MUTANT).
Asian Young Researchers Conference on Computational and Omics Biology 2010, March 10-12, 2010

MAQGene 0.9.4 – Pipeline for Mutant Discovery

MAQGene 0.9.4

:: DESCRIPTION

MAQGene is a software for C. elegans biologists with next-gen sequence data, facilitates genome-wide discovery of biologically meaningful mutations.MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.

::DEVELOPER

Hobert lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

  MAQGene

:: MORE INFORMATION

Citation

Nat Methods. 2009 Aug;6(8):549. doi: 10.1038/nmeth.f.260.
MAQGene: software to facilitate C. elegans mutant genome sequence analysis.
Bigelow H, Doitsidou M, Sarin S, Hobert O.