Conduct sequence analysis on raw electropherograms. Electropherograms must have the same cycle reads (x-axis values), and must be supplied in {A,C,G,T} order:

Conduct sequence analysis on a list of DNASequencing data objects:

Conduct sequence analysis on all data objects in all protocols in a list of protocols:

Given DNASequencing data collected from a sample with a known sequence, align the analysis result with the known sequence:

By default, AnalyzeDNASequencing uses the Phred base-calling algorithm. See the more information section of this documentation for additional details:

Inherit options from an existing analysis object. These objects will be overidden by any explicitly specified options in this analysis:

Trim a sequence after the 40th base:

If the TerminationNumberOFBases is larger than the length of the sequence, no trimming will occur:

When Trimming is set to Start or End, trimming will start from the requested direction and stop upon detecting the first occurence of one of the sequences in TerminationSequence:

The sequence will also be checked for any occurences of the reverse complements of sequences in TermationSequence:

When trimming is set to Both, the longest contiguous subsequence between termination sequences (or the sequence ends) will be returned:

When Trimming is Start or End, trim from the specified direction until the resulting trimmed sequence has a total unassignable base count less than 2:

When Trimming is Both, find the longest contiguous subsequence with a total unassignable base count lower than 2:

All bases with indices greater than this index will be trimmed:

All bases with indices less than this index will be trimmed:

By default, no trimming is performed:

Trim only the start (5') of the sequence:

Trim only the end (3') of the sequence:

Trim both ends of the sequence:

Trim sequence where subsequences (or their reverse complements) in TerminationSequence are identified in the called sequence. See option TerminationSequence for more information:

Trim sequence by base indices, trimming all bases before the 10th base and after the 60th base:

Trim sequence after a set number of bases. This trimming method is only compatible with Trimming->End:

Trim until the trimmed sequence has a total unassingable base count lower than a set threshold:

Trim such that the trimmed sequence contains no windows of 3 contiguous bases in which more than 50 Percent of the bases cannot be assigned ("N"):

By default, bases which fall below a quality score threshold will be assigned the letter "N":

Set UnassignedBases->False to force assignment of all bases, regardless of quality score:

Base assignments with a quality score below this threshold will be considered unassigned ("N") when UnassignedBases->True:

Set the size of contiguous runs of bases to check during window trimming. Here, ensure all contiguous runs of 20 bases in the trimmed sequence contain no more than 5% unassignable bases:

Set the maximum allowable percentage of unassignable bases in each contiguous window. Here, ensure all contiguous runs of 20 bases in the trimmed sequence contain no more than 5% unassignable bases:

Warning message if Trimming options are incompatible with the requested TrimmingMethod:

When both TrimBeforeIndex and TrimAfterIndex are specified, TrimBeforeIndex must be less than TrimAfterIndex. No trimming will occur if this condition is not met:

When Window trimming is used, the Window size must be between 2 and the length of the sequence:

All four sequencing traces corresponding to the same sequencing experimental run must have the same cycle reads (each trace must have the same x-values):

Warning if the requested sequence algorithm (e.g. Phred) does not support identification of mixed bases:

Warning message if TrimmingMethod->PrimerTerminus is requested and TerminationSequence->Automatic, but no PCR primer associated with the input(s) can be resolved:

The NumberOfBases trimming method is only compatible with Trimming->End, and will be defaulted to End if set to either Start or Both:

Warning if no satisfactory trimming can be found, e.g. a start trim in which there are no contiguous windows of 20 bases with greater than 1% unassignable bases:

Warning message if Trimming is not set or set to None, but other trimming options were requested:

If TrimBeforeIndex is out of bounds, then it will be defaulted to 1 and no trimming will occur:

If TrimAfterIndex is out of bounds, then it will be defaulted to the length of the sequence and no trimming will occur:

The UnassignableBases trimming method cannot be used if UnassignedBases is set to False:

The Window trimming method cannot be used if UnassignedBases is set to False:

If raw chromatogram data with unrecognized or incompatible units is provided, units will be ignored: