Download CodonCode Aligner User Manual

CodonCode Aligner User Manual
The number you set this way for the codonStart tag is the nucleotide number at this position.
Note: Keep in mind that the codonStart tag identifies the start of the first complete codon in this exon.
Therefore:
1. You must add "codingSequence" tags before adding the "codonStart" tag.
2. The codonStart tag must be in the first three bases of a "codingSequence" tag.
3. You can add only one codonStart tag per gene in your reference sequence.
4. If your reference sequence has several exons, the codonStart tag must be added to the first exon in the
reference sequence. For example, if your reference sequence contains exons 4 and 5, add the codonStart tag to
exon 4.
5. When specifying a base number in the codonStart tag, the number refers to the nucleotide in the cDNA
sequence. Therefore, the number must give a remainder of 1 when divided by 3 (e.g. 1, 4, 7, 10, ..., 3301,
3304,....).
Aligner will show a warning dialog when any one of these conditions is not met.
The easiest way to get the correct codingSequence and codonStart tags is by importing the reference
sequence from a text file in Genbank format. CodonCode Aligner will use the "CDS" features in the
Genbank file and add corresponding codingSequence and codonStart tags.
If you have more than one coding sequence region defined, Aligner will automatically keep track of the
reading frame as the base numbering; mutations in introns will be annotated using the standard "n+x" or "n-y"
numbering. Here is an example:
Numbering the Coding Sequence
96