CodonCode Aligner - AbsoluteAstronomy.com

CodonCode Aligner is a commercial application for DNA sequence assembly

Sequence assembly

In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...

, sequence alignment

Sequence alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...

, and editing on Mac OS X

Mac OS X

Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

and Windows

Microsoft Windows

Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

Features

Chromatogram editing, end clipping, and vector trimming.
Sequence assembly
Sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...

and contig editing
Aligning cDNA against genomic templates
Sequence alignment
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...

and editing.
Alignment of contigs to each other with ClustalW, MUSCLE, or built-in algorithms.
Mutation detection, including detection of heterozygous single-nucleotide polymorphism.
Analysis of heterozygous insertions and deletions.
Start online BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...

searches.
Restriction analysis - find and view restriction cut sites.
Trace sharpening.
Support for Phred
Phred base calling
Phred base-calling is a computer program for identifying a base sequence from a fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, Phred produced significantly fewer errors in the data sets examined...

, Phrap
Phrap
Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package.- History :Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the Human Genome Project...

, ClustalW, and MUSCLE.

History

The first beta version of CodonCode Aligner was released in April 2003, followed by the first full version in June 2003. Major upgrades were released in 2003, 2004, 2005, 2006, 2007, and 2008.

In April 2009, CodonCode Aligner had been cited in more than 400 scientific publications. Citations cover a wide variety of biomedical research areas, including HIV research,, biogeography and environmental biology, DNA methylation studies, genetic diseases, clinical microbiology, and evolution research and phylogenetics.

Features

History

External links

See also