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BioSoftwares

Bioinformatics Tools – Solutions – Services

Avogadro – advanced molecular editor

Avogadro is a new, open source molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture. While still in beta, the recent 0.9.7 release brings ...

BioClipse

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based ...

BioConductor

Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages. It has ...

A-MADMAN: Annotation-based MicroArray DataMeta ANalysis tool

Posted by primoto On October - 3 - 2010
A-MADMAN is an open source web application and gene chip analysis automation framework for annotation-based  meta-analysis of data from public repositories (NCBI GEO). A-MADMAN allows retrieval, annotation, organization and analysis of gene expression data from public repository. It automates several analysis steps to be accomplished to setup a working environment for conducting meta-analyses, without giving up power and flexibility. A-MADMAN supports a collaborative working style for local or geographically dispersed teams through LAN or Internet deployment options, but can be...
Comparative genomics study the evolution of gene organization, which in the past years was by the fast growing number of full genome sequences available in public repositories. Most of the available bioinformatics tools for visualization and comparison of genomes are restricted to two or three genomes at a time, which is a significant limitation in the field of comparative genomics. Recently (this month) a new phylogenetic software was announced – Genomicus. It provides functionality of a synteny browser, which can represent and compare unlimited numbers of genomes in a broad phylogenetic view....

BioEdit – sequence alignment editor

Posted by primoto On September - 12 - 2009
BioEdit easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student who knows how frustrating and time consuming it can be to rely upon word-processors and command-line programs for sequence manipulation. BioEdit is intended to supply a single program that can handle most simple sequence and alignment editing and manipulation functions that researchers are likely to do on a daily basis, as well as a few basic sequences analyses. BioEdit offers a variety of useful features: Four modes of manual alignment: select and slide, dynamic grab and drag,...

NoteExpress – scientific information manager

Posted by primoto On September - 11 - 2009
NoteExpress is a perfect assistant and information manager for researchers, scholars, students, and librarians. NoteExpress is designed to help you organize research notes and bibliographic references, generate bibliographies automatically, search and capture bibliographic data from Internet with efficiency and ease. NoteExpress is well integrated with Microsoft Word. It can format bibliographies in many popular styles. NoteExpress works the same as many other bibliograhic softwares but with many additional efficient features like: Manage bibliographic data and notes with efficiency Organize academic...

FastPCR – an integrated tool for PCR primers design

Posted by primoto On September - 10 - 2009
The FastPCR software is an integrated tools environment that provides comprehensive facilities for designing any kind of PCR primers for standard, long distance, inverse, real-time PCR (LUX and self-reporting), multiplex PCR, group-specific PCR (common primers for given N target sequences), unique PCR (design of specific (unique) PCR primers for each sequence); single primer PCR (design of PCR primers from close located inverted repeat), automatically detecting SSR loci and direct PCR primer design, amino acid sequence degenerate PCR and more. The software consists of a data editor; build-in commands...

MAExplorer – MicroArray Explorer

Posted by primoto On September - 7 - 2009
The Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases. It may be freely  downloaded and run as a  stand-alone application on your computer. The exploratory data analysis environment provides tools for the  data-mining of quantitative expression profiles across multiple microarrays. With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified...

Ondex – data integration platform

Posted by primoto On September - 3 - 2009
Gathering and managing data from diverse and heterogeneous datasets is central to many systems approaches to biology. Systems biologists need to easily identify and gather the information they require and then integrate and analysis the experimental and reference data sets which can come from myriad databases with a wide variety of formats and access methods. The Ondex data integration platform enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex uses a rich and flexible core data structure, which has the ability to bring...

Avogadro – advanced molecular editor

Posted by primoto On September - 2 - 2009
Avogadro is a new, open source molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture. While still in beta, the recent 0.9.7 release brings general usability to viewing and editing molecules. You can quickly export graphics to PNG, JPEG, or even POV-Ray rendering, or copy from the editor and paste a transparent PNG into programs like OmniGraffle. Avogadro supports reading from over 80 chemical file formats, courtesy of the Open Babel library. Current...

SOAP2: an improved ultrafast tool for short read alignment

Posted by primoto On August - 5 - 2009
SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20–30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple...
The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers. This toolbar provides access to major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data...

About Us

BioSoftwares is entirely dedicated on providing the latest information related to bioinformatics tools, solutions and services. BioSoftwares hosts an up-to-date software database, containing the latest versions of freely available applications and complete solutions for sequence analysis and annotation, gene expression clustering, advanced biological information retrieval and text mining. BioSoftwares evaluates the best available solutions in field of interest with in depth reviews of the applications functionalities and performance. Stay tuned to BioSoftwares for the latest news and trends in the field of applied bioinformatics!