Tag: Analysis Tool

PEAT / PEATDB 2.3 / PEATSA – Protein Engineering Analysis Tool

PEAT / PEATDB 2.3 / PEATSA

:: DESCRIPTION

PEAT is a collection of software that aids researchers in the field of protein analysis, engineering and design.

PEATDB (Protein Engineering Analysis Tool – Database) is a workbench for protein studies that provides some of the functions of a Laboratory Information Management System (LIMS) integrated with analysis tools.

PEATSA (Protein Engineering Analysis Tool – Structure Analysisis) a part of the PEAT suite of programs for storing, analysing and predicting biophysical data on proteins

::DEVELOPER

PEAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 PEAT

:: MORE INFORMATION

Citation

Proteins. 2011 Jan;79(1):165-78. doi: 10.1002/prot.22870.
Integrated prediction of the effect of mutations on multiple protein characteristics.
Johnston MA1, Søndergaard CR, Nielsen JE.

Proteins: From Birth to Death 21st Annual Symposium of The Protein Society, July 21-25, 2007, Boston, MA, USA
Georgi N, Farrell D, O’Meara F, Webb H, Tynan-Connolly BM, Bjarnadottir U, Soendergaard C, Nielsen JE
Structural analysis of datasets from protein engineering studies using PEAT

Getgo – A Simple Gene Enrichment analysis tool

Getgo

:: DESCRIPTION

GetGo is a tool of looking at enrichment of human genes in GO terms, pathways, and other clusters.

::DEVELOPER

Russell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Boldt K, et al..
An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.
Nat Commun. 2016 May 13;7:11491. doi: 10.1038/ncomms11491. PMID: 27173435; PMCID: PMC4869170.

MetaMeta 1.2.0 – Integrating Metagenome analysis tools to improve Taxonomic Profiling

MetaMeta 1.2.0

:: DESCRIPTION

MetaMeta is a pipeline to execute and integrate results from metagenome analysis tools. It provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample.

::DEVELOPER

Vitor C. Piro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaMeta

:: MORE INFORMATION

Citation

Piro VC, Matschkowski M, Renard BY.
MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.
Microbiome. 2017 Aug 14;5(1):101. doi: 10.1186/s40168-017-0318-y. PMID: 28807044; PMCID: PMC5557516.

HBAT 1.1 – Hydrogen Bond Analysis Tool

HBAT 1.1

:: DESCRIPTION

HBAT (Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph).

::DEVELOPER

Abhishek Tiwari & Sunil Kumar Panigrahi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HBAT

:: MORE INFORMATION

Citation

HBAT: a complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures.
Tiwari A, Panigrahi SK.
In Silico Biol. 2007;7(6):651-61.

csnpAnalysis 1.01 – PANTHER Coding SNP Analysis tool

csnpAnalysis 1.01

:: DESCRIPTION

 csnpAnalysis is a software to estimate the likelihood that a particular nonsynonymous (amino-acid changing) coding SNP will cause a functional impact to the protein.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 csnpAnalysis

:: MORE INFORMATION

Citation

Paul D. Thomas, et al. 2006.
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucl. Acids Res.34: W645-W650.

Encore 1.1 – GWAS and Biological Data Analysis tool

Encore 1.1

:: DESCRIPTION

Encore is a free, open-source command-line tool for analysis of GWAS (SNP) and other types of biological data.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Encore

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Sep;37(6):614-21. doi: 10.1002/gepi.21739. Epub 2013 Jun 5.
Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.
Davis NA1, Lareau CA, White BC, Pandey A, Wiley G, Montgomery CG, Gaffney PM, McKinney BA.

GATK 4.2.2.0 – Analysis Tools for Next-generation DNA Sequencers

GATK 4.2.2.0

:: DESCRIPTION

GATK (The Genome Analysis Toolkit) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GATK

:: MORE INFORMATION

Citation

Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nature Genetics 43, 491–498 (2011) doi:10.1038/ng.806

FX 1.0.5 – RNA-Seq analysis tool on the Cloud

FX 1.0.5

:: DESCRIPTION

FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.

::DEVELOPER

Genomic Medicine Institute, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17.
FX: an RNA-Seq analysis tool on the cloud.
Hong D1, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.

CLUSTERnGO v0.31 – Gene Expression Analysis Tool

CLUSTERnGO v0.31

:: DESCRIPTION

CnG (CLUSTERnGO) is a gene expression analysis tool that clusters gene (or protein) expression profiles, and extracts their GO enrichments.

::DEVELOPER

CnG team

:: SCREENSHOTS

CnG

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • QT

:: DOWNLOAD

 CnG

:: MORE INFORMATION

Citation

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.
Fidaner IB, Cankorur-Cetinkaya A, Dikicioglu D, Kirdar B, Cemgil AT, Oliver SG.
Bioinformatics. 2015 Sep 26. pii: btv532.

ESTate 0.5 – Expressed Sequence Tag Analysis Tools Etc

ESTate 0.5

:: DESCRIPTION

ESTate (Expressed Sequence Tag Analysis Tools Etc) is a package for EST analysis.

::DEVELOPER

Guy Slater (gslater@hgmp.mrc.ac.uk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Mac OsX/ Linux
  • C Complier

:: DOWNLOAD

  ESTate

:: MORE INFORMATION