Editor's Picks
- Develops powerful but easy to use Macintosh applications for Molecular Biologists to simplify and speed up the analysis, manipulation, assembly and documentation of DNA and protein sequences. MacVector is a comprehensive Macintosh sequence analysis application that provides sequence editing, primer design, internet database.
- Geneious Prime is a powerful bioinformatics software solution packed with fundamental molecular biology and sequence analysis tools. Perform a wide-range of cloning and primer design operations within one interface. Take charge with industry-leading assembly and mapping algorithms, and superior visualizations.
BioEdit - a free and very popular free sequence alignment editor for Windows. Has not been actively developed for several years, but still gets excellent reviews.
Free Dna Sequence Analysis Software For Mac Os
CodonCode Aligner - A powerful sequence alignment program for Windows and Mac OS X. Free demo downloads (no forms), 30-day fully functional trial.
The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. CodonCode Aligner 5.1.5 a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Program for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis. Sequence Manipulation Suite: JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. Superlink: Genetic linkage analysis with input-output relationships similar to those in standard.
What is Sequencher for Mac. Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently used.
MEGA - A free tool for sequence alignment and phylogenetic tree building and analysis. Integrated web interface for BLAST searches and GenBank browsing.
Free Sequence Alignment Software
Clustal - Perhaps the most commonly used tool for multiple sequence alignments. Available with a graphical user interface (ClustalX) or with a command line interface (ClustalW).
MUSCLE - A newer multiple sequence alignment program that often gives better alignments that Clustal, and is substantially faster for large data sets. No graphical user interface; public domain, available as source code.
Se-Al - An older sequence alignment editor for Mac OS X. Not updated since 2002, but still popular.
JAligner - Java implementation of the Smith-Waterman algorithm for pairwise alignments.
Mesquite - Software for evolutionary biology. Most functions are for post-alignment analysis like phylogenetic tree analysis, but also useful to view and manipulate sequence alignments.
Commercial Software For Sequence Alignment
Sequencher - A widely used sequence alignment and assembly package that started out as a program for the 'classic' Macintosh. Prices for licenses are not listed at the web site, but typically start at several thousand dollars. A demo version is available after filling out a web form, but does not allow saving.
DNASTAR Lasergene / MegAligner - Another popular program. Has separate modules for sequence assembly and multiple sequence alignments, as well as other modules for primer design, gene finding, and sequence editing. Trials available through web forms, prices comparable to Sequencher (depending on the number of modules purchased).
Vector NTI - Gained popularity when the program was made freely available to academic users, a policy that was ended in 2008. The current (4/18/09) list price for a 3-year academic license for Vector NTI is $1975.00 (with discounts of about 30% being offered).
MacVector - Another program package with many functions that has been around for a long time. Academic licenses cost $2,000, with discounts for additional licenses. However, advanced assembly based on PHRAP requires additional license fees.
CodonCode Aligner - Newer software for sequence alignment and sequence assembly on Windows and Mac OS X. Free trial downloads. Published prices, significantly less expensive than other popular packages. One useful and unique feature is the ability to align assembled contigs with Clustal or MUSCLE to create 'contigs of contigs'.
ONLINE ANALYSIS TOOLS
(INTERNET RESOURCES for MOLECULAR BIOLOGISTS)
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Analysis of nucleotide and protein sequence data was initially restricted to those with access to complicated mainframe or expensive desktop computer programs (for example PC/GENE, Lasergene, MacVector, Accelrys etc.). The availability of online tools permits even the novice molecular biologist the opportunity to derive a considerable amount of useful nformation from nucleotide or protein sequence data. For those with no experience I have provided three sequences: (a) a DNA sequence, (b) a protein sequence, and (c) four protein sequences presented in FASTA format. Prior to trying out a Web Site select the sequence and copy to clipboard. Each of the items in blue text is hyperlinked to a site on the Web. Each of these Web Sites has a box into which you can 'Paste' your sequence. Click on the button labeled 'Search,' 'Run' or 'Submit.' If in doubt use the default setting that the sites provide, but for the more adventuresome some of the sites offer the chance of modifying the search strategy.
ONLINE RESOURCES(tutorials and glossaries) - Needs work
TERTIARY STRUCTURE PREDICTIONS OF SACCHARIDES
ALIGNMENTS
CONVERT SEQUENCE(upper to low case, complement, reverse, RNA to DNA)
COMPOSITION
DNA MOTIFS
HOMOLOGY SEARCHES
MELTING TEMPERATURE (Tm)
PCR PRIMER DESIGN
PHYLOGENY
PROMOTERS
REPEATS & SECONDARY STRUCTURE
RESTRICTION ENDONUCLEASE SITES
TRANSLATION (GENERAL)
TRANSLATION (EUKARYOTIC GENES) (identification of introns and exons)
TRANSCRIPTION FACTORS
TOOLS FOR WHOLE GENOME ANALYSIS
ALIGNMENTS
COMPOSITION & CHEMISTRY
HOMOLOGY SEARCHES
MOTIFS
PHYLOGENY
QUATERNARY STRUCTURE PREDICTIONS
SECONDARY STRUCTURE PREDICTIONS
TERTIARY STRUCTURE PREDICTIONS
RNA ANALYSIS
PROMOTERS & TERMINATORS
TRANSCRIPTION FACTORS
Free Dna Sequence Analysis Software For Mac Download
BUFFERS
CENTRIFUGATION CALCULATIONS
GENERAL MOLECULAR BIOLOGY CALCULATIONS
META SITES FOR DNA & PROTEIN ANALYSIS
SEQUENCE CLEANUP & CONVERSION
ONLINE GRAPHICS
Dna software, free download
WINDOWS- & JAVA or PERL-BASED PROGRAMS- free molecular biology programs
DOWNLOADING SEQUENCES FROM GENBANK & MANIPULATING THEM IN BIOEDIT
The Bio-Web: Resources for Molecular and Cell Biologists is a non-commercial, educational site with the only purpose of facilitating access to biology-related information over the internet.
CREATED BY:Dr. Andrew M. Kropinski,Departments ofFood Science; and, Pathobiology University of Guelph,Guelph, Ontario, N1G 2W1 CANADA
Problems and suggestions: Contact - Andrew M. Kropinski (Email: Phage.Canada (at) gmail.com)