User Manuals

Use this link to access JAX Synteny Browser's user manual as a PDF.

Use this link to access two use cases for JAX Synteny Browser as a PDF.

Data Sources and Formats

Data Type File Name File Format File Source
1. Syntenic Relationships
1.1. Human-Mouse Syntenic Blocks MouseMineSynteny.blocks custom Mouse Mine
 
2. Genomic Features (gene, QTL, mRNA, ...)
2.1. Human Features - Genes NCBI_Human_forSynteny.gff3 GFF3 NCBI
2.2. Mouse Features - Genes MGI_GenomeFeature_forSynteny.gff3 GFF3 MGI
2.3. Mouse Features - QTL QTL_JBrowse.gff3 GFF3 N/A
 
3. Homologous Feature Pairings
3.1. Human to Mouse Homologous Gene Pairings MMHomologs.tsv custom MouseMine
 
4. Ontologies
4.1. Mouse GO (Gene Ontology) go-basic.obo OBO Genome Ontology Consortium
4.2. Human GO (Gene Ontology) go-basic.obo OBO Genome Ontology Consortium
4.3. Mouse MP (Mammalian Phenotype) MPheno_OBO.ontology OBO MGI
4.4. Human DO (Disease Ontology) HumanDO.obo OBO The OBO Foundry
 
5. Annotations (QTL, genes, mRNA, ...)
5.1. Human GO to Human Genes goa_human.gaf GAF2 NCBI
5.2. Human DO to Human Genes MGI_DO.rpt GAF2 MGI
5.3. Mouse GO to Species Genes gene_association.mgi GAF2 MGI
5.4. Mouse MP to Mouse Genes MouseMP_to_gene.txt custom MGI