About the Chimp genome

Assembly

chimpanzeeThis site provides a data set based on the March 2006 Pan_troglodytes-2.1 6x shotgun assembly from the Chimpanzee Sequencing Consortium headed by the GSC (St. Louis) and The Broad Institute (MIT).

The chimpanzee 2.1 assembly is a merge of the initial 4X made in collaboration with the Broad Institute at MIT and Harvard and an additional (2X) whole genome coverage from the WUGSC (St. Louis) utilizing a combination of whole genome plasmid reads as well as fosmid and BAC end sequences.

This release of the assembly has the following properties:

Chromosome numbering

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.

Annotation

The genome was aligned to human NCBI36 by UCSC using BLASTz. These alignments were used to transfer human ensembl gene structures (Human Build 36f) to chimpanzee. 92% of the chimp-specific proteins were aligned to the chimp genome in a first layer of annotation. The 8% missing correspond to fragments or proteins that contain stop codons in the assembled genome