NFINgb - Nothobranchius furzeri Genome Browser

NFINgb Nothobranchius furzeri Genome Browser

The Nothobranchius furzeri Information Network Genome Browser (NFINgb) provides access to the latest genome assembly and annotation of the short-lived teleost fish Nothobranchius furzeri generated by the Genome Analysis group of the Leibniz Institute on Aging - Fritz Lipmann Institute.

The following genome assemblies are currently maintained in NFINgb:

Assembly	Accession	Sequences	Total length	N50	Access
GRZ Assembly (05/2015)	PRJEB5837 (NCBI, ENA)*	5,896	1.24Gb	57.3Mb	Click here

* Note: The assembly there is named "Nfu_20140520" but is identical with the version listed here (05/2015)

Downloads

Genome sequence, gene and repeat annotation and variation are available for download:

GRZ Assembly (05/2015)

Description	Format
Sequence
Genome sequence, with repeats masked	softmasked FASTA, hardmasked FASTA
Protein sequences (gene models 22.09.2015; 59,154 sequences)	FASTA
Protein-coding transcript sequences (gene models 22.09.2015; 59,154 sequences)	FASTA
CDS sequences (gene models 22.09.2015; 59,154 sequences)	FASTA
The repeat library used for masking the genome assembly	FASTA
Independent PacBio BAC assemblies of X and Y allels at the sex determining region (see Supplemental Data S1I)	FASTA
Annotation
Dispersed repeats, identified by RepeatMasker	GFF3, ALIGN
Tandem repeats, identified by TandemRepeatsFinder	GFF3
Models of protein-coding, miRNA and non-protein-coding genes (22.09.2015; 27,552 genes)	GFF3
Models of protein-coding and miRNA genes (22.09.2015; 26,739 genes)	GFF3, GTF
Models of protein-coding genes, subset (30.06.2014; 26,141 genes)	GFF3, GTF
Models of protein-coding genes, subset (22.04.2014; 23,546 genes)	GFF3, GTF
Noncoding elements conserved in N. furzeri, medaka, platyfish, stickleback, tetraodon and zebrafish	GFF3
Micro RNA annotation* (Update 18.11.2019: Track integrated into the browser. Cross reference to mirBase not yet established.)	GFF3
Noncoding RNA annotation* (Update 19.11.2019: Track integrated into the browser.)	GFF3
Tab-separated table of protein-coding gene models (22.09.2015)	CSV
Gene Ontology ids and terms for protein-coding gene models (22.09.2015)	CSV
Models of genes predicted at NCBI/RefSeq (Integration on 21.11.2019)	GFF3
Variation
Variation and genotypes in GRZ	VCF
Variation and genotypes in MZM-0410	VCF
Variation and genotypes in MZM-0403	VCF
Variation and genotypes in MZZW-0701	VCF

Publications

Please cite the following publication if you use data from this browser:
Reichwald, K, et al.: Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish, Cell, Volume 163, Issue 6, 3 December 2015, Pages 1527-1538, ISSN 0092-8674, doi: 10.1016/j.cell.2015.10.071.

*If you refer to the microRNA or non-codingRNA tracks please cite the following publication:
Baumgart, M, et al.: A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri, BMC Genomics, 2017, 18:693, doi: 10.1186/s12864-017-3951-8.

Further Links

NFINtb - Nothobranchius furzeri Transcriptome Browser
NFINbs - Nothobranchius furzeri BLAST server
The Nothobranchius furzeri Information Network website

Help

How to retrieve the sequence of a particular genomic region using the N. furzeri genome browser: PDF
If you need help with using this web site or the genome browser, please contact nfinhelp@nothobranchius.info.