Photo courtesy of J.R. Kaplan
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Macaca mulatta Photo courtesy of J.R. Kaplan |
The Jan. 2005 Rhesus monkey or Rhesus macaque (Macaca mulatta) preliminary assembly,
Mmul_0.1, was obtained from the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC). The sequencing and assembly of the Macaca mulatta genome is a project of the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the J. Craig Venter Institute Joint Technology Center, and the Genome Sequencing Center at Washington University School of Medicine, St. Louis.
A genome position can be specified by the accession number of a sequenced mRNA or EST, a scaffold coordinate range, a gene identifier, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the rhesus genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
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| SCAFFOLD80001 | Displays all of SCAFFOLD80001 (on an unmapped genome assembly) | |
| SCAFFOLD544:26,374-29,857 | Displays a region of SCAFFOLD544:26,374-29,857 with a cluster of Spliced ESTs | |
| SCAFFOLD544:26,374+2000 | Displays a region of SCAFFOLD544 that spans 2000 bases, starting with position 26,374 | |
| CN647194 | Displays EST with GenBank accession CN647194 | |
| AF518412 | Displays mRNA with GenBank accession AF518412 | |
| PRNP | Displays human and chimp RefSeq gene PRNP aligned to SCAFFOLD5559 | |
| leptin | Lists mRNAs associated with leptin receptors | |
| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| Scinicariello,F. | Lists mRNAs deposited by co-author F. Scinicariello | |
| Use this last format for author queries. Although GenBank requires the search format Scinicariello F, internally it uses the format Scinicariello,F.. | ||
Mmul_0.1 is a preliminary assembly using whole genome shotgun (WGS) reads from small and medium insert clones. The following assembly information was taken from the BCM HGSC README that accompanies the Mmul_0.1 download data.
This release was produced by assembling whole genome shotgun reads with the Atlas genome assembly system at BCM HGSC. Several WGS libraries, with inserts of 2-4 kb and 10 kb, were used to produce the data. About 14.58 million reads were used in the assembly, representing about 12.6 Gb of sequence and about 4.6x coverage of the (clonable) macaque genome. Highly-repeated sequences and sequences from BAC clones were omitted from this assembly and will be placed in a subsequent version of the draft sequence.
The Atlas assembler produces a set of contigs and scaffolds. Scaffolds include sequence contigs that can be ordered and oriented with respect to each other, as well as isolated contigs that could not be linked (single contig scaffolds or singletons). Reads that clustered into groups of two or less were not assembled, and highly-repetitive reads that clustered into groups of more than 18 were assembled separately. The N50 of the contigs is 10.5 kb; the N50 of the scaffolds is 79.7 kb. The total length of all contigs is 2.69 Gb, or 2.81 Gb when the gaps between contigs are included.
This is a draft sequence and may contain errors; therefore, users should exercise caution. Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps (e.g. due to polymorphisms) creating artificial duplications. However base accuracy in contigs is usually very high with most errors near the ends of contigs.
To review information on the quality of this assembly, see the Mmul_0.1 README. For general information about the rhesus monkey sequencing project, see the Baylor Rhesus Monkey Project 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 rheMac1 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.