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This site provides a data set based on the November
13th 2003 4x shotgun assembly from the Chimpanzee Sequencing
Consortium headed by the GSC (St. Louis) and The Broad Institute (MIT).
The assembly is a merge of a "modified de novo" (MDN) assembly from the ARACHNE group, which used the human genome to establish that particular inserts were not chimeric, and a separate "validated chimp-on-human" (VCH) assembly which took the chimp reads which align uniquely to human, formed them into contigs via this alignment, and removed contigs which failed a two-haplotype consistency check.
Shared reads were used to align the two assemblies to each other, and where they were consistent, the VCH sequence was transferred to the MDN, resulting in the released merged assembly.
This release of the assembly has the following properties:
As of Release 35 we have changed the chimpanzee chromosome numbering to match the new primate standard proposed by E.H. McConkey (Cytogenetics and Genome Research, 105:157-158) and endorsed by the International Chimpanzee Genome Consortium.
The genome was aligned to human by UCSC using BLASTz. These alignments were used to transfer human gene structures (Human Build 34d) to chimpanzee. Owing to the low coverage commensurate with a 4x shotgun, there will inevitably be some mis-assemblies and mis-placements; however with better data it is expected that most chimpanzee genes will align with near-identical human genes.
The following updates have been made to ensembl_compara.
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ContigView navigation has been enhanced with new popup menus and navigation features.
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The following xrefs have been added/updated.
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| Assembly: | PanTro 1.0, Nov 2003 |
| Genebuild: | Ensembl, Mar 2005 |
| Database version: | 38.3b |
| Known genes: | 20,150 |
| Novel genes: | 2,325 |
| RNA genes: | 3,476 |
| Genscan gene predictions: | 129,588 |
| Gene exons: | 226,066 |
| Gene transcripts: | 43,000 |
| Base Pairs: | 2,733,948,177 |
| Golden Path Length: | 2,733,223,211 |
| Most common InterPro domains: | Top 40 Top 500 |
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
