NCBI annotated gene vs. genes from the original genome assembly

Overview
Analysis NameNCBI annotated gene vs. genes from the original genome assembly
Methodblat
Sourcefiles from NCBI and the original genome assemblies
Date performed2017-11-28

Blat was performed with NCBI annotated sequences against the sequences from the original genome assemblies with 90% identity and the best hit (lowest evalue) was chosen. The table below provides the source files, % of sequences in the query with match, and the result files. The result files in each section provides blat results with hyperlinks to NCBI and GDR gene/protein pages.

Malus x domestica

Blat was performed with NCBI annotated sequences against the sequences from the original genome assemblies with 90% identity and the best hit (lowest evalue) was chosen. The table below provides the source files, % of sequences in the query with match, and the result files. The result files below provides blat results with hyperlinks to NCBI and GDR gene/protein pages.

  NCBI annotated sequences seq from the original assembly files with the best match % seq with match
mRNA  GCF_000148765.1_MalDomGD1.0_rna.fna Malus_x_domestica.v1.0.consensus_CDS.fa.gz NCBI_Mdomestica.v1.0.cds.best.xlsx 98.16     
  GCF_000148765.1_MalDomGD1.0_rna.fna GDDH13_1-1_mrna.fasta.gz NCBI_GDDH13_1-1_mrna.best.xlsx 97.36
Protein GCF_000148765.1_MalDomGD1.0_protein.faa Malus_x_domestica.v1.0.consensus_peptide.fa.gz NCBI_Mdomestica.v1.0.prot.best.xlsx 99.17
  GCF_000148765.1_MalDomGD1.0_protein.faa GDDH13_1-1_prot.fasta.gz NCBI_GDDH13_1-1_prot.best.xlsx 98.07

MDP_vs_ncbi_by_cds_with_loc.xlsx: Blast results performed by FEM (Fondazione Edmund Mach)

Fragaria vesca

Blat was performed with NCBI annotated sequences against the sequences from the original genome assemblies with 90% identity and the best hit (lowest evalue) was chosen. The table below provides the source files, % of sequences in the query with match, and the result files. The result files below provides blat results with hyperlinks to NCBI and GDR gene/protein pages.

  NCBI annotated sequences seq from the original assembly files with the best match % seq with match
mRNA  GCF_000184155.1_FraVesHawaii_1.0_rna.fna fvesca_v1.0_genemark_abinitio.fna.gz NCBI_fvesca_v1.0_abinitio.best.xlsx 97.32    
  GCF_000184155.1_FraVesHawaii_1.0_rna.fna fvesca_v1.0_genemark_hybrid.fna.gz NCBI_fvesca_v1.0_hybrid.best.xlsx 97.83
Protein GCF_000184155.1_FraVesHawaii_1.0_protein.faa  fvesca_v1.0_genemark_abinitio.faa.gz NCBI_fvesca_v1.0_abinitio_prot.best.xlsx 98.92
  GCF_000184155.1_FraVesHawaii_1.0_protein.faa fvesca_v1.0_genemark_hybrid.faa.gz NCBI_fvesca_v1.0_hybrid_prot.best.xlsx 99.12
Prunus persica

Blat was performed with NCBI annotated sequences against the sequences from the original genome assemblies with 90% identity and the best hit (lowest evalue) was chosen. The table below provides the source files, % of sequences in the query with match, and the result files. The result files below provides blat results with hyperlinks to NCBI and GDR gene/protein pages.

  NCBI annotated sequences seq from the original assembly files with the best match % seq with match
mRNA  GCF_000346465.2_Prunus_persica_NCBIv2_rna.fna Prunus_persica_v2.0.a1.allTrs.cds.fa.gz NCBI_Ppersica_v2.0.a1.allTrs.best.xlsx 95.64   
Protein GCF_000346465.2_Prunus_persica_NCBIv2_protein.faa Prunus_persica_v2.0.a1.allTrs.pep.fa.gz NCBI_Ppersica_v2.0.a1.allTrs.pep.best.xlsx 96.31