| 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/$db/sedefSegDups/sedefSegDups.bb -chrom=chr6 -start=0 -end=1000000 stdout ++Please 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;