Tandem Graph Dina Sokol Ramin Rakhamimov http tandem

Tandem. Graph Dina Sokol Ramin Rakhamimov http: //tandem. sci. brooklyn. cuny. edu Department of Computer and Information Science Brooklyn College CUNY BIOCOMP ’ 09: Las Vegas Nevada

Tandem. Graph A graphical tool for modeling string regularities Graphs tandem repeats generated by various genome parsers. Enables user to see all data in a single view. Provides easy navigation of data (shifting, scaling, zooming. . . ) Licensed by AFPL, you can contribute and modify according to your needs.

Why we need Tandem. Graph? Graphical presentations of string patterns enable easy and efficient methods of analysis. When input is large text presentation, abstract statistics is hard to deduce. Graphical tools enable the user to intuitively pinpoint individual or global patterns. Areas of high concentration as well as sparse areas are easily discernable.

Tandem Repeats Tandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other. In DNA, tandem repeats are used for disease diagnosis, mapping studies, and human identity testing. 50% of the human genome consists of repeated sequences, of which some are tandem repeats. TRED – (A tool developed by our team, Justin Tojeira, Dr. Dina Sokol) parses genomes and generates a list of tandem repeats found.

Example ATTCGATTCG… The sequence ATTCG is repeated three or more times.

Example Alignment Start: 72001 End: 72021 Length: 21 Period: 2. 1 Repeats: 10 Errors: 1 72001 AA 72002 72003 AA 72004 72005 AA 72006 72007 AA 72008 72009 AA 72010 72011 AA 72012 72013 AA 72014 72015 AA 72016 A-A 72017 AGA 72019 72020 AG 72021

Textual/Graphical Comparison Running TRED on Chromosome 1 of Homo Sapiens generated 91, 815 repeats. Generating about 1, 000 paginated pages per chromosome. Using the graphical approach, all 91, 815 repeats are displayed within a single view.

First 15 repeats of 91, 815

All repeats of 91, 815 using Tandem. Graph

Features of Tandem. Graph Load tandem repeats data from our in-house database. Navigate around desired regions through selecting, shifting and zooming widgets. Switch between triangle or trapezoid representation. Select individual repeats. View individual period sizes and number of errors. View actual alignment of the tandem repeats.

Loading a Chromosome

Selecting a Region

Zooming in on the Region

Incremental Zoom

Switch to Trapezoid View

Select a Repeat

View Alignment

Shift Left or Right

Future of Tandem. Graph Apply to other fields of edit distance outside of Biology. Enable the use of other proprietary/standard input formats. Integrate with textual presentations for a more fine tuned control.

Questions