This is the first release of the high-coverage 6.79X assembly of the Guinea Pig (Cavia porcellus). The genome sequencing and assembly is provided by the Broad Institute.
The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for contigs is 80.58 kb and the N50 of the supercontigs is 27.41 Mb. The total length of all contigs is 2.66 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 2.72 Gb.
Due to the lack of Guineapig protein and cDNA resources, the majority of the gene models are based on Genewise alignments of proteins from mammals. Alignments made from Guineapig proteins had UTR added using Guineapig cDNAs. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.
Mammalian Genome Project
Cavia porcellus is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. A subset of these species are being sequenced in further depth. The aim is to increase our understanding of functional elements, especially in the human genome.
General information about this species can be found in Wikipedia.
|Assembly||cavPor3, Mar 2008|
|Golden Path Length|
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
|Genebuild method||Full genebuild|
|Genebuild started||Mar 2008|
|Genebuild released||Sep 2008|
|Genebuild last updated/patched||May 2010|
Genes and/or transcript that contains an open reading frame (ORF).
|Non coding genes||5,963|
|Small non coding genes|
Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.
|Misc non coding genes||1,511|
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.||26,129|
|Genscan gene predictions||53,615|