CodonCode Aligner is a commercial application for DNA
sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one g ...
,
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 biology, structural, or evolutionary relationships between ...
, and editing on
Mac OS X
macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...
and
Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...
.
Features
Features include
chromatogram
In chemical analysis, chromatography is a laboratory technique for the Separation process, separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it ...
editing, end clipping, and vector trimming,
sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one g ...
and contig editing, aligning
cDNA
In genetics, complementary DNA (cDNA) is DNA that was reverse transcribed (via reverse transcriptase) from an RNA (e.g., messenger RNA or microRNA). cDNA exists in both single-stranded and double-stranded forms and in both natural and engin ...
against genomic templates,
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 biology, structural, or evolutionary relationships between ...
and editing, alignment of contigs to each other with
ClustalW
Clustal is a computer program used for multiple sequence alignment in bioinformatics. The software and its algorithms have gone through several iterations, with ClustalΩ (Omega) being the latest version . It is available as standalone software, ...
,
MUSCLE
Muscle is a soft tissue, one of the four basic types of animal tissue. There are three types of muscle tissue in vertebrates: skeletal muscle, cardiac muscle, and smooth muscle. Muscle tissue gives skeletal muscles the ability to muscle contra ...
, or built-in algorithms, mutation detection, including detection of heterozygous
single-nucleotide polymorphism
In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a ...
, analysis of heterozygous insertions and deletions, start online
BLAST
Blast or The Blast may refer to:
*Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
*A planned explosion in a mine, ...
searches, restriction analysis (find and view restriction cut sites), RFLP analysis, virtual cloning, including Gibson Assembly, restriction cloning, and TA and TOPO cloning, primer design, phylogenetic trees, difference tables, trace sharpening, and support for
Phred,
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 t ...
,
ClustalW
Clustal is a computer program used for multiple sequence alignment in bioinformatics. The software and its algorithms have gone through several iterations, with ClustalΩ (Omega) being the latest version . It is available as standalone software, ...
, and
MUSCLE
Muscle is a soft tissue, one of the four basic types of animal tissue. There are three types of muscle tissue in vertebrates: skeletal muscle, cardiac muscle, and smooth muscle. Muscle tissue gives skeletal muscles the ability to muscle contra ...
.
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, 2006, 2007, 2009, 2010, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2021, 2023, and 2024.
In April 2009, CodonCode Aligner had been cited in more than 400 scientific publications. In 2025 CodonCode Aligner has been cited in thousands of peer-reviewed 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.
[ ]
See also
*
Phred base calling
*
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 t ...
*
Consed
References
{{reflist
External links
CodonCode Aligner homepage
Bioinformatics software
Computational science