Photo courtesy of NHGRI (press photos)
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Pongo pygmaeus abelii Photo courtesy of NHGRI (press photos) |
The Jul. 2007 Pongo pygmaeus abelii draft assembly (WUSTL version Pongo_albelii-2.0.2) was produced by the Genome Sequencing Center at Washington University School of Medicine in St. Louis (WUSTL). For more information about this assembly, see P_pygmaeus_2.0.2 in the NCBI Assembly database.
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the orangutan genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chr22 | Displays all of chromosome 22 | |
| chr1:1-1000000 | Displays first million bases of chr 1 | |
| chr1:1000000+2000 | Displays a region of chr 1 that spans 2000 bases, starting with position 1000000 | |
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| AF512949 | Displays region of mRNA with GenBank accession number AF512949 | |
| CR542506 | Displays region of EST with GenBank accession CR542506 on chr 22 | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
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| paabo | Lists mRNAs deposited by scientist named Paabo | |
| Wiemann,S. | Lists mRNAs deposited by co-author S. Wiemann | |
| Use this last format for author queries. Although GenBank requires the search format Wiemann S, internally it uses the format Wiemann,S.. | ||
The Pongo pygmaeus abelii assembly (6X coverage) consists of whole genome shotgun data from primary donor-derived reads obtained from "Susie", a female Sumatran orangutan housed at the Gladys Porter Zoo in Brownsville, TX. The combined sequence reads were assembled using the PCAP software (Huang, 2003) and filtered for all known non-orangutan sequence contaminants using stringent parameters derived by eliminating detectable global mis-assemblies larger than 50 kb. Mis-assemblies (interchromosomal cross-overs) were determined by aligning the orangutan genome against the human genome. Sequences were obtained from plasmids, fosmids, and BAC-end sequences from CHORI-276, also obtained from "Susie". A fingerprint map with a target of 12X clone coverage is currently in progress.
The assembly data were aligned against the human genome at UCSC (B. Raney) using BLASTZ (Schwartz, 2003) to align and score non-repetitive orangutan regions against repeat-masked human sequence. The alignment chains differentiated between orthologous and paralogous alignments (Kent, 2003), and only "reciprocal best" alignments were retained in the final alignment set. The orangutan AGP files were generated from these alignments in a manner similar to that already described (The Chimpanzee Genome Sequencing and Analysis Consortium, 2005). Documented inversions based primarily on FISH data (Rocchi, personal communication) as well as inversions suggested by the assembly and supported by additional mapping data (e.g. fosmid end sequences against the human assembly, (Chen and Eichler, personal communication)) were introduced. The alignments to human chromosome 2 were separated into organutan chromosomes 2A and 2B. Finally, 78 finished BAC (CHORI-273) clones were integrated into the final chromosomal sequences.
Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. Click the "Sequences" link above for a list of the chromosomes available in this assembly. The mitochondrial sequence is also available as the virtual chromosome "chrM". For more information about this assembly, see the WUSTL Pongo abelii web page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The orangutan browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.