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Pundamilia nyererei assembly and gene annotation

Assembly

The PunNye1.0 assembly was submitted by Broad Institute on December 2011. The assembly is on scaffold level, consisting of 68,053 contigs assembled into 7,236 scaffolds. 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 the contigs is 22,622 while the scaffold N50 is 2,525,540.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000239375.1

Gene annotation

Haplochromis nyererei is a species of cichlid endemic to Lake Victoria in Africa. This species can reach a length of 7.7 centimetres (3.0 in) SL. The derives its name from political activist Julius Nyerere.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPunNye1.0, INSDC Assembly GCA_000239375.1, Dec 2011
Base Pairs830,133,247
Golden Path Length830,133,247
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,501
Non coding genes744
Small non coding genes726
Long non coding genes3
Misc non coding genes15
Pseudogenes27
Gene transcripts32,924

Other

Genscan gene predictions36,022

About this species