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Biomedical subjects

J D Parsons

Publications and source records attributed to J D Parsons.

8 recordsLinked to original sources
PubMed1996

Lane tracking software for four-color fluorescence-based electrophoretic gel images.

Software to track sample lanes automatically in four-color, fluorescence-based, electrophoretic gel images has been developed for application in large-scale DNA sequencing projects. Lanes and lane boundaries are tracked by analyzing a first difference approximation to the gradient of a vertically integrated and processed "brightness" profile. Initially lanes are located in a region of the gel image selected for good horizontal lane spacing and signal strength. The software uses models of expected lane and interlane spacing and lateral lane behavior to maintain accurate tracking on imperfect gels. In areas where intensity-based tracking is difficult, interpixel column correlation is also used to locate and define lane features. Summary statistics and compressed-in-time images are generated for user evaluation of tracking performance. The software developed has been tested successfully on gel images with degradations including significant horizontal lane motion (curving) and image artifacts, and is now in full-scale use in our sequencing projects.

Algorithms↗
PubMed1995

Improved tools for DNA comparison and clustering.

DNA sequence clustering is an effective aid of the comprehension, summarization and compression of DNA sequence databases. Previous work created programs suitable for the comparison and clustering of cDNA sequences but new enhanced programs have been written to cluster genomic DNA fragments, large EST projects, and entire DNA databases. Three new programs (ICAtools) are discussed: ICAass, N2tool, and ICAmatches. ICAass has been used to compress the EMBL database by hiding or removing sequences with various degrees of redundancy. It also has the fastest database querying mode. N2tool provides fast and sensitive clustering of genomic fragment databases on the basis of small areas of local similarity. N2tool has proven utility in the discovery of contaminating vector or other artefactual sequence when the potential contaminant is not otherwise known. ICAmatches is a new cluster analysis program that uses a novel alignment style to present multiple alignment summaries. All the tools are convenient to use because they share a common memory-frugal index format and accept most DNA sequence formats directly.

Algorithms↗
PubMed1995

Miropeats: graphical DNA sequence comparisons.

Miropeats displays DNA sequence similarity information graphically. The program discovers regions of similarity amongst any set of DNA sequences and then draws a graphic that summarizes the length, location and relative orientations of any repeated sequences. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing large-scale sequence similarities on a single page of PostScript graphics. Miropeats has been applied estensively to help understand shotgun assembly projects, to check cosmid overlaps and to perform inter-genomic comparisons.

Algorithms↗
PubMed1992

Clustering cDNA sequences.

A set of programs has been written to quantify the similarities between large numbers of cDNA sequences. This information is used to cluster similar sequences together. The main program can cluster thousands of cDNA sequences per day using a novel, computationally inexpensive algorithm. The clustering information is kept in a small index file so that disk storage requirements are negligible. Using this index file, subsidiary programs create various views and statistical summaries of the entire cDNA sequence collection.

Algorithms↗