CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. Features include chromatogram...

most often aligned to every codon. The resulting amino acid (or stop codon) probabilities for each codon are displayed in a genetic code logo. As of...

platforms. It is fully integrated into software programs such as CodonCode Aligner, DNASTAR's Lasergene, Geneious, and MacVector, and is also available...

S2CID 205420247. Hauswedell H, Singer J, Reinert K (2014-09-01). "Lambda: the local aligner for massive biological data". Bioinformatics. 30 (17): 349–355. doi:10...

display, end clipping, and consensus determination; other programs like CodonCode Aligner also implement quality-based consensus methods. Quality scores are...

interface, the commercial programs MacVector (for Mac OS X only) and CodonCode Aligner (for Mac OS X and Microsoft Windows) are available. A detailed (albeit...

distributed commercially by CodonCode Corporation, and used to perform the "Call bases" function in the program CodonCode Aligner. It is also used by the...

reading of the codons after the mutation to code for different amino acids. The frameshift mutation will also alter the first stop codon ("UAA", "UGA"...

haploid/diploid genomes PacBio/Oxford Nanopore reads 2001 / 2018 OS link CodonCode Aligner Assemble fragments using local, end-to-end, or large gap (cDNA to...

the UGA codon it affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine...

open-source software portal Genome Compiler Phred base calling Phrap Consed CodonCode Aligner MacVector UGENE Vector NTI Bonfield JK, Whitwham A (2010). "Gap5—editing...

Proprietary, freeware for academic use No Command line Official website CodonCode Aligner no, but can read, add & show structure annotations Clustal, MUSCLE...

signals. For example, the codon CAG codes for the amino acid glutamine and the codon UAA is a stop codon. The standard genetic code is described as degenerate...

of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome...

triplets called codons. Each of those triplets codes for a specific amino acid.[citation needed] The ribosome molecules translate this code to a specific...

proteins and the sense codons (i.e., the 61 codons that encode amino acids in the standard genetic code) for aligned protein-coding gene sequences. In fact...

annotation, such as base and codon counts. In fact, codon usage was the main strategy used by several early protein coding sequence (CDS) prediction methods...

Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region. There are 64 possible codons (four possible...

genetic code of the mitochondrial genome is an unusual type 4 code, found across different prokaryotic and eukaryotic groups, in which the UGA codon codes for...

a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution...

lactidomycin to prevent any further initiation. This allows the starting codon of the mRNAs throughout the cell lysate to be analyzed, which has been used...

in which nucleotides or amino acids are represented using single-letter codes. The format allows for sequence names and comments to precede the sequences...

technique is useful because the genetic code itself is degenerate, meaning several different codons can code for the same amino acid. This allows different...

methionine as the start (initiation) codon AUG. Each codon is translated into a single amino acid. The code itself is considered degenerate, meaning that a...

Model Syn-Nonsynonymous - Sequences are compared codon-by-codon, only available for protein coding sequences. Nei-Gojobori Method Modified Nei-Gojobori...

Yurchenko V, Rogozin IB (February 2021). "Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events". International...

two codons (ATG and GCA). However, CUB is a major driving factor of 3-mer usage bias (accounting for up to ⅓ of it, since ⅓ of the k-mers in a coding region...

also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAG, TAA, and TGA codons, (UAG, UAA, and UGA on the mRNA)...

the rRNA structure affects the entire ribosome in its ability to match a codon with its anticodon in tRNA selection as well as decode mRNA. Ribosomal RNA's...

protein.) This is primarily due to redundancy in the genetic code, which translates similar codons into similar amino acids. Furthermore, mutating an amino...