Category: Bioinformatics Platform

SeqVISTA 1.81 – Sequence Feature Visualization & Comparison

SeqVISTA 1.81

:: DESCRIPTION

SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. SeqVISTA  may be launched on a GenBank record by a single click of a button installed in the web browser.

::DEVELOPER

Zlab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

SeqVISTA

:: MORE INFORMATION

Citation:

Zhenjun Hu1 , Martin Frith , Tianhua Niu and Zhiping Weng ; “SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison” ;  BMC Bioinformatics 2003, 4:1doi:10.1186/1471-2105-4-1

 

LabtoolsQt 1.0.3 – Program for the Molecular Biological Lab

LabtoolsQt 1.0.3

:: DESCRIPTION

LabTools is a program for the molecular biological lab. It was developed to assist people by common calculations in the lab, e.g. DNA ligation ratios, oligo annealing temperatures in a PCR reaction, soloution calculator or unit conversions..

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LabTools

:: MORE INFORMATION

DIVERGENOME – Bioinformatics Platform to Assist Population Genetics and Genetic Epidemiology Studie

DIVERGENOME

:: DESCRIPTION

DIVERGENOME is a bioinformatics platform to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups.

DIVERGENOMEtools is a dynamic pipeline composed of a set of scripts, developed using a graph-based coordination algorithm and implemented in the programming language Perl.

::DEVELOPER

The Laboratory of Human Genetic Diversity (LDGH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 May;36(4):360-7. doi: 10.1002/gepi.21629. Epub 2012 Apr 16.
DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.
Magalhães WC1, Rodrigues MR, Silva D, Soares-Souza G, Iannini ML, Cerqueira GC, Faria-Campos AC, Tarazona-Santos E.

Oqtans 0.1 beta – Online Quantitative Transcriptome Analysis

Oqtans 0.1 beta

:: DESCRIPTION

Oqtans is an integrative online platform for quantitatively analyzing RNA-Seq experiments. It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Oqtans

:: MORE INFORMATION

Citation:

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G.
Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731.

Bioconductor 3.13 – Open Source Software for Bioinformatics

Bioconductor 3.13

:: DESCRIPTION

Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

::DEVELOPER

Bioconductor Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bioconductor

:: MORE INFORMATION

Publications

Geneious 2021.1 – Bioinformatics Software Suite

Geneious 2021.1

:: DESCRIPTION

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more.

::DEVELOPER

Biomatters Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Geneious

:: MORE INFORMATION

Citation

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A.
Bioinformatics. 2012 Jun 15;28(12):1647-9.

QIAGEN CLC Main Workbench 21.0.4 – Bioinformatics Workbench

QIAGEN CLC Main Workbench 21.0.4

:: DESCRIPTION

QIAGEN CLC Main Workbench is a bioinformatics workbench.CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

::DEVELOPER

QIAGEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

CLC Main Workbench

:: MORE INFORMATION

CloVR 1.0 RC9 – Automated Sequence Analysis from Your Desktop

CloVR 1.0 RC9

:: DESCRIPTION

CloVR is a desktop application that integrates state-of-the-art genomic tools in a robust, user friendly, and fully automated software package with optional support for cloud computing platforms. CloVR currently bundles push-button pipelines for microbial genomics, including single-genome projects, 16S rRNA sequence analysis, and metagenomic sequencing projects. Additional pipelines for comparative genome analysis, prokaryotic and eukaryotic RNA-sequencing and viral genomics are planned.

::DEVELOPER

Institute for Genome Sciences , University of Maryland School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CloVR

:: MORE INFORMATION

Citation:

Angiuoli SV, Matalka M, Gussman G, Galens K, Vangala M, Riley DR, Arze C, White JR, White O and Fricke WF.
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
BMC Bioinformatics. 2011 Aug;12:356.