The Bio-Web: Molecular and Cell Biology and Bioinformatics news, tools, books, resources and web applications development
Macintosh Software for Molecular Biology
GeneCoder is a comprehensive and customizable Molecular Biology Software package for use in molecular cloning and sequence analysis of DNA and protein sequences. Available for mac and windows OS.
XPlasMap is a DNA mapping program for MacOS 10.4 or higher. It draws plasmid or linear DNA maps, showing features such as genes, multiple cloning sites, and restriction sites. The maps are highly customizable: colors, styles, position, and overall appearance of features can be changed. Fragments can be copied or cut, and inserted into different maps or turned into maps on their own (virtual cloning). We have tested it here at cellbiol.com, it works, it's free. Great stuff.
EnzymeX helps molecular biologists to determine which restriction enzymes they should use to cut their DNA of interest. In addition, it gives all the specific properties of these enzymes so that you can make sure that every digestion is a success.
As the author says, "DNAid is not a heavyweight package which will run your 'just-sequenced gene' through every prediction or analysis algorithm in the known universe." However, it is a very usefull application that allows to perform all the basic manipulations of DNA sequences such as restriction mapping, translation, reverse-complement and others. Freeware, thanks to Frédéric Dardel
4Peaks is a program that help molecular biologists to visualize and edit their DNA sequence files. At last there is a decent solution for analyzing trace files on the MacOSX platform, taking another step away from slow and non-native programs from the MacOS9 period. Also, 4Peaks supports most commonly used sequence file formats right out of the box, you no longer have to convert them first using AppleScripts or other painstaking methods. Analyzing your sequence was never so much fun! Key features:
- Reading and writing of most common trace file formats.
- Direct access to both sequence and translation.
- Ability to edit and correct the sequence. Keep interesting parts only, or export your data as text or FASTA files.
- Quickly search for a sequence or translation, navigate through your file by selecting pieces of either sequence or translation.
A bit dated but still great full featured sequence manipulation application for the mac. Freeware. Unfortunately Strider will not run on recent Macs, as it requires a "Classic" environment. Will work great on older machines
Linux Software for Molecular Biology and Bioinformatics
Bio-Linux is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can also install Bio-Linux packages to handle new generation sequence data types
BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners, learners, students, staffs and Research scholars
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. Also check out the EMBOSS Administrator's Guide
Excellent summary of all you really need to know about linux commands, in one single page
PC Software for Molecular Biology and Bioinformatics
MB DNA Analysis
Features of MB: restriction analysis (incl. plasmid / linear DNA drawing), promoter, amino acids analysis, multiple sequence alignment tool (Needleman-Wunsch algorithm), dot plot, calculation of molecular weights and chemical properties of proteins, prediction of 3D structures for small amino acids sequences. Other features: estimation of isoelectric point for proteins and primer design.
EMBOSS for windows
This work is an attempt to make the EMBOSS package run on Windows PCs. EMBOSS is a free open source software set of high-quality sequence analysis programs mainly designed for the Unix operating system. The ambition of this work is to provide an easy-to-install and easy-to-use EMBOSS distribution for the Windows platform (NT, 2000 or XP).
CLC Sequence Viewer
CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. The software package is a community edition, available for Windows, Mac OS X, and Linux. Download is free of charge
Gene Designer 2.0
Gene Designer 2.0 encompasses a complete and visually rich set of tools to bring your creative ideas to completion
GenePalette is a powerful cross-platform and cross-species desktop application for genome sequence visualization and navigation. Users can download segments of genome sequence from NCBI’s GenBank database from a variety of organisms, preserving the gene annotation. Sequence elements of interest (transcription factor binding sites, other regulatory motifs, restriction enzyme sites, primer sequences, SNPs, microsatellites, etc.) can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation
Gene Designer 2.0
UGENE is a free open-source cross-platform bioinformatics software. It works perfectly on Windows, Mac OS and Linux and requires only a few clicks to install
PICKY is a software tool for selecting optimal oligonucleotides (oligos). PICKY allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. PICKY can also be used to analyze existing microarray probes and evaluate their design quality
RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench. RasTop wraps a user-friendly graphical interface around the "RasMol molecular engine"
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