Malus baccata genome v1.0 cds

Human-Readable NameMalus baccata genome v1.0 cds
Database NameMalus_baccata-v1.0.cds.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink

Malus baccata genome v1.0

Human-Readable NameMalus baccata genome v1.0
Database NameMalus_baccata-v1.0.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Malus baccata v1.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Malus baccata genome v1.0 proteins

Human-Readable NameMalus baccata genome v1.0 proteins
Database NameMalus_baccata-v1.0.proteins.faa
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for Malus baccata v1.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

About the Assembly

Malus baccata is one of four wild apple species that can hybridize with the cultivated apple species (Malus domestica). It is widely used in high-latitude apple-producing areas as a rootstock and breeding resource because of its disease resistance, and cold tolerance. A lack of a refe... [more]

Resource Titles: 
Assembly
Gene Predictions
Downloads
Homology
Functional Analysis
Resource Blocks: 

The Malus baccata Genome v1.0 assembly file is available in FASTA format.

Downloads

Scaffold (FASTA file) mbaccata-v1.0.fasta.gz

The Malus baccata v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) mbaccata-v1.0.proteins.fasta.gz
CDS (FASTA file) mbaccata-v1.0.CDs.fasta.gz
Genes (GFF3 file) mbaccata-v1.0.genes.gff3.gz

 

All assembly and annotation files are available for download by selecting the desired data type in the right-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

Homology of the Malus baccata genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Malus baccata v1.0 proteins with NCBI nr homologs (EXCEL file) mbaccata-v1.0_vs_nr.xlsx.gz
Malus baccata v1.0 proteins with NCBI nr (FASTA file) mbaccata-v1.0_vs_nr_hit.fasta.gz
Malus baccata v1.0 proteins without NCBI nr (FASTA file) mbaccata-v1.0_vs_nr_noHit.fasta.gz
Malus baccata v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) mbaccata-v1.0_vs_arabidopsis.xlsx.gz
Malus baccata v1.0 proteins with arabidopsis (Araport11) (FASTA file) mbaccata-v1.0_vs_arabidopsis_hit.fasta.gz
Malus baccata v1.0 proteins without arabidopsis (Araport11) (FASTA file) mbaccata-v1.0_vs_arabidopsis_noHit.fasta.gz
Malus baccata v1.0 proteins with SwissProt homologs (EXCEL file) mbaccata-v1.0_vs_swissprot.xlsx.gz
Malus baccata v1.0 proteins with SwissProt (FASTA file) mbaccata-v1.0_vs_swissprot_hit.fasta.gz
Malus baccata v1.0 proteins without SwissProt (FASTA file) mbaccata-v1.0_vs_swissprot_noHit.fasta.gz
Malus baccata v1.0 proteins with TrEMBL homologs (EXCEL file) mbaccata-v1.0_vs_trembl.xlsx.gz
Malus baccata v1.0 proteins with TrEMBL (FASTA file) mbaccata-v1.0_vs_trembl_hit.fasta.gz
Malus baccata v1.0 proteins without TrEMBL (FASTA file) mbaccata-v1.0_vs_trembl_noHit.fasta.gz

 

Functional annotation for the Malus baccata genome v1.0 are available for download below. The Malus baccata genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan mbaccata-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan mbaccata-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways mbaccata-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs mbaccata-v1.0_KEGG-pathways.xlsx.gz