Software:CodonCode Aligner
| Developer(s) | CodonCode Corporation |
|---|---|
| Stable release | 4.2.5
/ 2013 |
| Operating system | Mac OS X, Windows |
| Type | Bioinformatics |
| License | commercial; free for limited use (trace viewing & editing) |
| Website | http://www.codoncode.com/aligner |
CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows.
Features
Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA against genomic templates, sequence alignment 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 searches, restriction analysis (find and view restriction cut sites), trace sharpening, and support for Phred, Phrap, 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,[1][2][3] biogeography and environmental biology,[4][5] DNA methylation studies,[6] genetic diseases,[7][8][9] clinical microbiology,[10][11] and evolution research and phylogenetics.[12][13][14]
See also
References
- ↑ "Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells'Ć.". J Virol 80 (13): 6441–6457. 2006. doi:10.1128/JVI.00591-06. PMID 16775332.
- ↑ "Severe anaemia is not associated with HIV-1 env gene characteristics in Malawian children.". BMC Infect Dis 8: 26. 2008. doi:10.1186/1471-2334-8-26. PMID 18312662.
- ↑ "Frequent Intrapatient Recombination between Human Immunodeficiency Virus Type 1 R5 and X4 Envelopes: Implications for Coreceptor Switch'ñø.". J Virol 81 (7): 3369–3376. 2007. doi:10.1128/JVI.01295-06. PMID 17251288.
- ↑ "MHC class I characterization of Indonesian cynomolgus macaques.". Immunogenetics 60 (7): 339–351. 2008. doi:10.1007/s00251-008-0292-4. PMID 18504574.
- ↑ "Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)'Ć.". Appl Environ Microbiol 72 (5): 3626–3636. 2006. doi:10.1128/AEM.72.5.3626-3636.2006. PMID 16672511.
- ↑ "Direct detection of methylation in genomic DNA.". Nucleic Acids Res 33 (14): e124. 2005. doi:10.1093/nar/gni121. PMID 16091626.
- ↑ "Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6.". BMC Genet 9: 88. 2008. doi:10.1186/1471-2156-9-88. PMID 19099555.
- ↑ "Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes.". PLOS ONE 3 (8): e2907. 2008. doi:10.1371/journal.pone.0002907. PMID 18682798. Bibcode: 2008PLoSO...3.2907T.
- ↑ "3p-Syndrome Defines a Hearing Loss Locus in 3p25.3.". Hear Res 224 (1–2): 51–60. 2007. doi:10.1016/j.heares.2006.11.006. PMID 17208398.
- ↑ "Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry.". J Clin Microbiol 44 (6): 1963–1970. 2006. doi:10.1128/JCM.01959-05. PMID 16757585.
- ↑ "A Helicobacter pylori TolC Efflux Pump Confers Resistance to Metronidazole.". Antimicrob Agents Chemother 49 (4): 1477–1482. 2005. doi:10.1128/AAC.49.4.1477-1482.2005. PMID 15793129.
- ↑ "Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies.". Genetics 180 (3): 1567–1577. 2008. doi:10.1534/genetics.107.082982. PMID 18791259.
- ↑ "Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis.". Proc Biol Sci 274 (1617): 1481–1487. 2007. doi:10.1098/rspb.2007.0248. PMID 17426015.
- ↑ "Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?". PLOS ONE 2 (8): e728. 2007. doi:10.1371/journal.pone.0000728. PMID 17710128. Bibcode: 2007PLoSO...2..728S.
External links
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