Combining DNA and protein alignments to improve genome annotation with LiftOn

Table 4.

Genome assembly and annotation details for species analyzed in this study

Species Name GenBank accession Download link Annotation release date
Homo sapiens GRCh38.p14 GCA_000001405.29 https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2023_03/ March 21, 2023
Homo sapiens T2T-CHM13v2.0 GCA_009914755.4 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ August 27, 2024
Pan troglodytes mPanTro3-v1.1 GCA_028858775.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/ April 11, 2023
Mus musculus GRCm39 GCA_000001635.9 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/ February 8, 2024
Mus musculus NOD_SCID GCA_031763685.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/031/763/685/GCA_031763685.1_NOD_SCID/ NA
Rattus norvegicus mRatBN7.2 GCA_015227675.2 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/227/675/GCF_015227675.2_mRatBN7.2/ June 12, 2023
Apis mellifera Amel_HAv3.1 GCA_003254395.2 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/395/GCF_003254395.2_Amel_HAv3.1/ September 30, 2022
Apis mellifera ASM1932182v1 GCA_019321825.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/321/825/GCA_019321825.1_ASM1932182v1/ NA
Arabidopsis thaliana TAIR10.1 GCA_000001735.2 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/ June 16, 2023
Arabidopsis thaliana ASM2311539v1 GCA_023115395.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/115/395/GCA_023115395.1_ASM2311539v1/ NA
Oryza sativa IRGSP-1.0 GCA_001433935.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/433/935/GCF_001433935.1_IRGSP-1.0/ June 6, 2023
Oryza sativa ASM3414082v1 GCA_034140825.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/034/140/825/GCF_034140825.1_ASM3414082v1/ July 11, 2024
Drosophila melanogaster Release 6 plus ISO1 MT GCA_000001215.4 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/ December 27, 2023
Drosophila erecta DereRS2 GCA_003286155.2 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/286/155/GCF_003286155.1_DereRS2/ June 24, 2019
  • Note that for each species, the table includes the GenBank accession number, assembly name, FTP sites for assembly and annotation downloads, and annotation release dates.

This Article

  1. Genome Res. 35: 311-325

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