Promethease/Features

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The core literature retrieval function of Promethease makes an HTML report about your DNA. That most important feature is free. However there are several benefits to a paid report.

Compare this free report to a similar paid report.

Speed[edit]

A report can be generated in approximately 5 minutes. Free reports take closer to 4 hours.

UI2[edit]

UI2 allows you to filter and re-sort your data while a zoomable live graph visualizes the relationships.

Tab Delimited[edit]

A file such as this which can be opened by Excel and http://docs.google.com

Tag Cloud[edit]

A tag cloud visualization of the words in your report.

Desktop Only[edit]

Features below this point relate to comparing multiple genomes, and are only available in the Desktop version, not the web based version.

F1 Report[edit]

The ability to compare your genome to someone else's. It works well for 23andMe formatted files, but not yet for others such as Complete Genomics. F1 reports require additional time to generate. This is typically approximately 10minutes more for each pair of files.


Genomic Similarity[edit]

This part of the report shows pictures which highlight regions of similarity and difference between the two genomes. This can illustrate family relationships and patterns of genetic inheritance. For each chromosome there are 2 images created.

F1 self.png F1 parent child.png F1 unrelated1.png F1 sibling.png
self (or twins) parent-child unrelated siblings
Comparing a genome against itself results in a solid baby blue. Fully identical A parent compared to a child. Dark blue is a half-identical region Two unrelated people have a sprinkling of red across the whole chromosome Two siblings show alternating bands with and without red. Regions with red were not inherited the same parent, regions of solid blue are identical.

The Rectangle[edit]

One is a rectangle with size determined by the number of SNPs which were genotyped on that chromosome. Each SNP is presented in order in a pattern which 'snakes' so that the string 0123456789ABCEFH would be written as

012345
BA9876
CDEFGH

This method for visualizing DNA is simple to explain, but it can fool the eye. In the image above it would appear that 0 & B are as close together as 5 & 6.

The Other Shape[edit]

The other shape is a Hilbert Curve, which is a more complex way of laying down the DNA. It minimizes the false impression above. If you think you 'see' something in either image, it should be present in both images.


An analysis of twins using these images is at http://tech.pnosker.com/2011/03/30/our-genome-decoded-how-companies-like-23andme-are-advancing-the-field-of-personal-genomics/

Turned into a blanket by the Textile Museum Tilburg

Possible Offspring[edit]

This part of the report shows what genotypes are possible if these two genomes have children. It is similar to the top most part of a Promethease report, but with an extra field, 'Probability'. This will always be shown as 25% or 50%. Genotypes with 100% probability have no special label. The genotypes have been filtered to remove any which are also found in your file since there isn't much point in telling you all the places where your offspring could be like you.


Since User:Corpas mom had children with User:Corpas_dad their offspring should expect this report. If User:Corpas mom had instead had children with User:Manu Sporny her offspring would have this report. If User:Corpas mom had children with her own daughter then you would produce a report like this.

Family Report[edit]

This family report illustrates comparisons between members of a real family. Each column is a person, as is each row. The cells of the grid represent the results of offspring between these two individual. The cells of the diagonal represent that individual having children with "themselves" (also known as self-pairing or self-mating). This may seem like an error, but Promethease is also able to work for non-human genomes. Plants can produce offspring via Self-pollination. Even for humans it is one more way to look at and think about your own DNA, and in particular, about the concept of how many recessive alleles you carry.

Phasing[edit]

If you provide data for your mother and father, Promethease will generate an extra file with your phased data into a tab delimited file.


XML Batches[edit]

If you need to run many reports you might find it easier to prepare an .xml file which describes all the settings. See the exact syntax at Promethease/xml