The following colors are used to distinguish levels of similarity:
| less than 90% similarity | Purple |
| 90 - 98% similarity | Light to dark gray |
| 98 - 99% similarity | Yellow |
| greater than 99% similarity | Orange |
Sedef was run with default parameters on a RepeatMasked genome assembly. The resulting output (final.bed) was then converted into a browser friendly format (bed9 + extra fields).
The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our REST API, where the track name is sedefSegDups.
For automated analysis, the data may be downloaded from our download server as a bigBed file. The file for this track is called sedefSegDups.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:
bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hs1/sedefSegDups/sedefSegDups.bb -chrom=chr6 -start=0 -end=1000000 stdoutPlease refer to our mailing list archives for questions, or our Data Access FAQ for more information.
M. R. Vollger et al., Segmental duplications and their variation in a complete human genome. Science. 2022 April 1; eabj6965. DOI: 10.1126/science.abj6965
Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018 Sep 1;34(17):i706-i714. PMID: 30423092; PMC: PMC6129265