JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly

The files listed below are formatted for visualization in the Integrated Genome Browser, available from BioViz.org.

Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome Bioinformatics Table Browser. Each file is named for its corresponding table in the UCSC Genome database. See the annots.xml meta-data file in this directory for details.

Files with extension .gz were compressed and indexed using bgzip and tabix tools from htslib.org.

The file named X_tropicalis_Nov_2009.2bit contains sequence data and is from the UCSC Genome Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file genome.txt lists sequences and their sizes and was made from X_tropicalis_Nov_2009.2bit sequence file using twoBitInfo.

Both twoBitInfo and twoBitToFa are available from http://hgdownload.cse.ucsc.edu/admin/exe/.

	Name	Last modified	Size	Description
	Parent Directory		-
	X_tropicalis_Nov_2009_all_est.psl.gz	2023-06-16 13:41	50M	PSL (alignments) blat output file
	X_tropicalis_Nov_2009_all_est.psl.gz.tbi	2023-06-16 13:41	489K	Tabix index file
	X_tropicalis_Nov_2009_all_mrna.bed.gz	2023-06-16 13:41	960K	Annotation or junction file
	X_tropicalis_Nov_2009_refGene.bed.gz	2023-06-16 13:41	548K	Data from UCSC refGene table
	annots.xml	2025-03-11 10:01	1.2K	Annotation and data file list
	genome.txt	2023-06-16 13:41	275K	Chromosome lengths and assembly information