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Assembly from Fragments   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2007-05-02

Description

This track shows the draft assembly of the platypus genome. Combined whole genome shotgun plasmid, fosmid and BAC end sequence reads were assembled using the PCAP software (Huang, et al., 2003) using stringent parameters. After initial assembly with the PCAP software, "supercontigs" (ordered/oriented contigs; contigs are contiguous sequences not interrupted by gaps) were linked to the physical map (Washington University Genome Sequencing Center) using BAC end sequences and in silico digests of the sequence itself. The physical map, then, was used to organize the supercontigs into "ultracontigs" (ordered/oriented supercontigs). With the exception of those supercontigs with alignments at >95% identity to a platypus EST (Washington University Genome Sequencing Center), supercontigs smaller than 2 kb were removed from the data set prior to submission if they were >97% identical over >97% of their length to other ultracontigs larger than 2 kb or if they were deemed to be >95% repetitive (based on analysis using RECON (Bao and Eddy, 2002) for repeat identification). Further, singleton contigs (those not part of a supercontig or ultracontig) smaller than 500 bp that did not have an alignment of >95% identity to a platypus EST were not submitted.

In dense mode, this track depicts the contigs that make up the currently viewed chromosome or ultracontig. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within an ultracontig is always known; therefore, a line is drawn in the graphical display to bridge the blocks.

All components within this track are of fragment type "W": Whole Genome Shotgun contig.