Purpose of these web pages
This set of web pages contain the sequence analysis programs and are split into
This section contains quality control programs which detect and reject low quality
- ABI_QC screens AB1 files for the signal to noise ratio calculated by the
ABI base calling software.
- MaximumPhred calculates the maximum Phred score for a given length of sequence
for each Phred (*.phd.1) file in a folder. This data is compared to a user defined
cut off and the result is saved to a file.
- RegionOfInterest is similar to MaximumPhred except the user supplies a sequence
and the program calculates the average Phred score across this region in each Phred
- dbQC is an extension of MaximumPhred, storing the quality score data in an access
database which can then be queried to find trends and there possible cause in sequence
Currently this section contains:
- CpGViewer which aids analysis of bisulphite treated DNA sequences.
- Genescreen is a sequence variant detection and annotation program.
- gSNP is similar to QSVanalyser but genotypes SNPs in trace files.
- Illuminator is a program that analyses data from an Illumina clonal
sequencer, however unlike many clonal sequencing programs it is designed to screen one gene in many
people, rather than many genes in one person.
- FindReads searches a clonal sequencer fasta data files for sequences
containing user defined short sequence.
- Gene genotyper will screen a clonal sequencing fasta data file
against a list of know SNPs and output their genotypes.
- IlluminaQC reads all the *qseq.txt files in a folder and finds the average PHRED
score for each position in the sequence read
- MethyViewer is an updated version of CpGViewer and is able to
screen other methylation sites such as GpC, CpNpG or any user defined site.
- QSVanalyser calculates the relative ratio of two highly homologous
DNA sequences that differ at a few positions.