In order for Chromaseq to be able to process the chromatogram files so that Phred and Phrap can analyze them, Chromaseq needs to know the names of the primers associated with the various gene fragments or genes, and the relative direction of the primers. Other features in Chromaseq require the primer sequences. Currently, the only way to provide this information to Chromaseq is in a text file.
Primer Information File
This information is provided to Chromaseq in the form of a tab-delimited text file with one row for each primer. That row contains first the primer name, then the gene fragment name, then an F it is a forward primer or an R if it is a reverse primer, then the primer's sequence, and finally a semicolon. Thus, the format of this text file is as follows:
primer name <tab> fragment name <tab> F for forward or R for reverse <tab> primer sequence ;
primer name <tab> fragment name <tab> F for forward or R for reverse <tab> primer sequence ;
primer name <tab> fragment name <tab> F for forward or R for reverse <tab> primer sequence ;
Here is an example file, showing one forward and one reverse primer for the 18SrDNA gene, and four reverse primers for the CAD gene:
1055F 18SrDNA F GGTGGTGCATGGCCG ;
18L 18SrDNA R CACCYACGGAAACCTTGTTACGACTT ;
1098R CAD R TTNGGNAGYTGNCCNCCCAT ;
1098Ra CAD R TTRTTNGGNARYTGNCCNCCCAT ;
1098Ra CAD R TTRTTNGGNARYTGNCCNCCCAT ;
1250R CAD R TCRTTNTTYTTWGCRATYAAYTGCAT ;
An XML format is being developed for this information, but it is not yet supported.