Overview of SeedMatchR Annotation Databases

Introduction

This entry covers which annotations are available for the 3 model species used in SeedMatchR (human, mouse, rat). SeedMatchR requires information on the GTF for gene > transcript annotations as well as the sequences that correspond to the features of interest being searched. These can be generated independently by the user or they can be loaded with the SeedMatchR::load_annotations function. This function will load the predefined annotations based on the species of interest, the filtering criteria, and features of interest.

NOTES:

In order to use rnor7, you must have R 4.3.0 or greater installed. This is because AnnotationHub ≥ 3.8.0 is required.
rnor6 and mm10 cannot be used with the ensembldb::TxIsCanonicalFilter therefore the canonical argument for SeedMatchR::load_annotations must be set to FALSE.
rnor6 and rnor7 cannot be used with ensembldb::TxSupportLevelFilter. Therefore this value should not be passed to the function SeedMatchR::load_annotations when working with the rat transcriptome.

Current Annotation Options

Species	SeedMatchR arg	Reference Build	ENSEMBL Build	Release Date	2bit ID	ensembldb
Human	hg38	GRCh38.p13	109	February 2023	AH106283	AH109606
Rat	rnor6	Rnor_v6.0	104	May 2011	AH93578	AH95846
Rat	rnor7	Rnor_v7.2	109	February 2023	AH106786	AH109732
Rat	rnor7.113	Rnor_v7.2	113	October 2024	AH106786	AH119437
Mouse	mm39	GRCm39	109	February 2023	AH106440	AH109655
Mouse	mm10	GRCm38	102	October 2020	AH88475	AH89211

Functions for working with annotations and building transcriptomes for queries

Load data for Rnor7

annodb <- load_annotations("rnor7", feature.type = "exons", protein.coding = FALSE, canonical = F, return_gene_name = F)
#> Build AnnotationFilter for transcript features based on the following parameters: 
#> Keep only standard chroms: TRUE
#> Remove rows with NA in transcript ID: TRUE
#> Keep only protein coding genes and transcripts: FALSE
#> Filtering for transcripts with support level: FALSE
#> Keep only the ENSEMBL canonical transcript: FALSE
#> Filtering for specific genes: FALSE
#> Filtering for specific transcripts: FALSE
#> Filtering for specific gene symbols: FALSE
#> Filtering for specific entrez id: FALSE
#> Loading annotations from AnnotationHub for rnor7
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> require("rtracklayer")
#> Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
#> 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> require("ensembldb")
#> Extracting exons from ensembldb object.
#> Extracting sequences for each feature.
#> Keeping sequences that are >= 8

How annotations were retrieved

Selecting GTF

The GTF files were selected to have the full DNA sequence visible without any type of masking of repeats. These files have names like Mus_musculus.GRCm39.109.gtf.

Selecting `.2bit` DNA sequences

The .2bit files were selected to have the full DNA sequence visible without any type of masking of repeats. These files have names like Homo_sapiens.GRCh38.dna.primary_assembly.2bit. For Rat, there was no file that was named as the dna.primary_assembly, instead we had to choose from dna_sm.primary_assembly which is the soft-masked version of the genome that accounts for repeats.

Code for querying `AnnotationHub` for references

Hg38

`.2bit`

AnnotationHub::query(ah, c("GRCh38", "2bit"))
#> AnnotationHub with 120 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Homo sapiens, homo sapiens
#> # $rdataclass: TwoBitFile
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH49722"]]' 
#> 
#>              title                                           
#>   AH49722  | Homo_sapiens.GRCh38.cdna.all.2bit               
#>   AH49723  | Homo_sapiens.GRCh38.dna.primary_assembly.2bit   
#>   AH49724  | Homo_sapiens.GRCh38.dna_rm.primary_assembly.2bit
#>   AH49725  | Homo_sapiens.GRCh38.dna_sm.primary_assembly.2bit
#>   AH49726  | Homo_sapiens.GRCh38.ncrna.2bit                  
#>   ...        ...                                             
#>   AH106282 | Homo_sapiens.GRCh38.cdna.all.2bit               
#>   AH106283 | Homo_sapiens.GRCh38.dna.primary_assembly.2bit   
#>   AH106284 | Homo_sapiens.GRCh38.dna_rm.primary_assembly.2bit
#>   AH106285 | Homo_sapiens.GRCh38.dna_sm.primary_assembly.2bit
#>   AH106286 | Homo_sapiens.GRCh38.ncrna.2bit

`ensembldb`

version 110 for GRCh38.p13

AnnotationHub::query(ah, c("GRCh38", "110"))
#> AnnotationHub with 1 record
#> # snapshotDate(): 2025-04-08
#> # names(): AH113665
#> # $dataprovider: Ensembl
#> # $species: Homo sapiens
#> # $rdataclass: EnsDb
#> # $rdatadateadded: 2023-04-25
#> # $title: Ensembl 110 EnsDb for Homo sapiens
#> # $description: Gene and protein annotations for Homo sapiens based on Ensem...
#> # $taxonomyid: 9606
#> # $genome: GRCh38
#> # $sourcetype: ensembl
#> # $sourceurl: http://www.ensembl.org
#> # $sourcesize: NA
#> # $tags: c("110", "Annotation", "AnnotationHubSoftware", "Coverage",
#> #   "DataImport", "EnsDb", "Ensembl", "Gene", "Protein", "Sequencing",
#> #   "Transcript") 
#> # retrieve record with 'object[["AH113665"]]'

Version 80 for GRCh38.p2

AnnotationHub::query(ah, c("GRCh38", "80"))
#> AnnotationHub with 1 record
#> # snapshotDate(): 2025-04-08
#> # names(): AH47066
#> # $dataprovider: Ensembl
#> # $species: Homo sapiens
#> # $rdataclass: GRanges
#> # $rdatadateadded: 2015-05-22
#> # $title: Homo_sapiens.GRCh38.80.gtf
#> # $description: Gene Annotation for Homo sapiens
#> # $taxonomyid: 9606
#> # $genome: GRCh38
#> # $sourcetype: GTF
#> # $sourceurl: ftp://ftp.ensembl.org/pub/release-80/gtf/homo_sapiens/Homo_sap...
#> # $sourcesize: 44733199
#> # $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation") 
#> # retrieve record with 'object[["AH47066"]]'

Rat

`.2bit`

Rnor6

query(ah, c("Rnor", "release-104"))
#> AnnotationHub with 7 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: rattus norvegicus
#> # $rdataclass: TwoBitFile, GRanges
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH92418"]]' 
#> 
#>             title                                          
#>   AH92418 | Rattus_norvegicus.Rnor_6.0.104.abinitio.gtf    
#>   AH92419 | Rattus_norvegicus.Rnor_6.0.104.chr.gtf         
#>   AH92420 | Rattus_norvegicus.Rnor_6.0.104.gtf             
#>   AH93576 | Rattus_norvegicus.Rnor_6.0.cdna.all.2bit       
#>   AH93577 | Rattus_norvegicus.Rnor_6.0.dna_rm.toplevel.2bit
#>   AH93578 | Rattus_norvegicus.Rnor_6.0.dna_sm.toplevel.2bit
#>   AH93579 | Rattus_norvegicus.Rnor_6.0.ncrna.2bit

Rnor7

query(ah, c("Rattus", ".2bit"))
#> AnnotationHub with 106 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl, UCSC
#> # $species: Rattus norvegicus, rattus norvegicus
#> # $rdataclass: TwoBitFile
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH14021"]]' 
#> 
#>              title                                           
#>   AH14021  | rn6.2bit                                        
#>   AH14022  | rn5.2bit                                        
#>   AH14023  | rn4.2bit                                        
#>   AH49867  | Rattus_norvegicus.Rnor_6.0.cdna.all.2bit        
#>   AH49868  | Rattus_norvegicus.Rnor_6.0.dna_rm.toplevel.2bit 
#>   ...        ...                                             
#>   AH104348 | Rattus_norvegicus.mRatBN7.2.ncrna.2bit          
#>   AH106784 | Rattus_norvegicus.mRatBN7.2.cdna.all.2bit       
#>   AH106785 | Rattus_norvegicus.mRatBN7.2.dna_rm.toplevel.2bit
#>   AH106786 | Rattus_norvegicus.mRatBN7.2.dna_sm.toplevel.2bit
#>   AH106787 | Rattus_norvegicus.mRatBN7.2.ncrna.2bit

`ensembldb`

Rnor6

query(ah, c("rat", 104, "ensdb"))
#> AnnotationHub with 6 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Sparus aurata, Rattus norvegicus, Mesocricetus auratus, Kryptole...
#> # $rdataclass: EnsDb
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH95677"]]' 
#> 
#>             title                                        
#>   AH95677 | Ensembl 104 EnsDb for Carassius auratus      
#>   AH95725 | Ensembl 104 EnsDb for Echeneis naucrates     
#>   AH95749 | Ensembl 104 EnsDb for Kryptolebias marmoratus
#>   AH95762 | Ensembl 104 EnsDb for Mesocricetus auratus   
#>   AH95846 | Ensembl 104 EnsDb for Rattus norvegicus      
#>   AH95850 | Ensembl 104 EnsDb for Sparus aurata

Rnor7

query(ah, c("rat", 109, "ensdb"))
#> AnnotationHub with 6 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Sparus aurata, Rattus norvegicus, Mesocricetus auratus, Kryptole...
#> # $rdataclass: EnsDb
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH109518"]]' 
#> 
#>              title                                        
#>   AH109518 | Ensembl 109 EnsDb for Carassius auratus      
#>   AH109583 | Ensembl 109 EnsDb for Echeneis naucrates     
#>   AH109611 | Ensembl 109 EnsDb for Kryptolebias marmoratus
#>   AH109625 | Ensembl 109 EnsDb for Mesocricetus auratus   
#>   AH109732 | Ensembl 109 EnsDb for Rattus norvegicus      
#>   AH109736 | Ensembl 109 EnsDb for Sparus aurata

Mouse

`.2bit`

mm39 or GCRm39

query(ah, c("GRCm39", ".2bit"))
#> AnnotationHub with 25 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: mus musculus
#> # $rdataclass: TwoBitFile
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH90962"]]' 
#> 
#>              title                                           
#>   AH90962  | Mus_musculus.GRCm39.cdna.all.2bit               
#>   AH90963  | Mus_musculus.GRCm39.dna.primary_assembly.2bit   
#>   AH90964  | Mus_musculus.GRCm39.dna_rm.primary_assembly.2bit
#>   AH90965  | Mus_musculus.GRCm39.dna_sm.primary_assembly.2bit
#>   AH90966  | Mus_musculus.GRCm39.ncrna.2bit                  
#>   ...        ...                                             
#>   AH106439 | Mus_musculus.GRCm39.cdna.all.2bit               
#>   AH106440 | Mus_musculus.GRCm39.dna.primary_assembly.2bit   
#>   AH106441 | Mus_musculus.GRCm39.dna_rm.primary_assembly.2bit
#>   AH106442 | Mus_musculus.GRCm39.dna_sm.primary_assembly.2bit
#>   AH106443 | Mus_musculus.GRCm39.ncrna.2bit

mm10 or GRCm38

query(ah, c("GRCm38", ".2bit"))
#> AnnotationHub with 95 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Mus musculus, mus musculus
#> # $rdataclass: TwoBitFile
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH49772"]]' 
#> 
#>             title                                           
#>   AH49772 | Mus_musculus.GRCm38.cdna.all.2bit               
#>   AH49773 | Mus_musculus.GRCm38.dna.primary_assembly.2bit   
#>   AH49774 | Mus_musculus.GRCm38.dna_rm.primary_assembly.2bit
#>   AH49775 | Mus_musculus.GRCm38.dna_sm.primary_assembly.2bit
#>   AH49776 | Mus_musculus.GRCm38.ncrna.2bit                  
#>   ...       ...                                             
#>   AH88474 | Mus_musculus.GRCm38.cdna.all.2bit               
#>   AH88475 | Mus_musculus.GRCm38.dna.primary_assembly.2bit   
#>   AH88476 | Mus_musculus.GRCm38.dna_rm.primary_assembly.2bit
#>   AH88477 | Mus_musculus.GRCm38.dna_sm.primary_assembly.2bit
#>   AH88478 | Mus_musculus.GRCm38.ncrna.2bit

`ensembldb`

mm39 or GRCm39

query(ah, c("mus", 104, "ensdb"))
#> AnnotationHub with 11 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Ursus maritimus, Scophthalmus maximus, Prolemur simus, Periophth...
#> # $rdataclass: EnsDb
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH95670"]]' 
#> 
#>             title                                              
#>   AH95670 | Ensembl 104 EnsDb for Balaenoptera musculus        
#>   AH95763 | Ensembl 104 EnsDb for Mus caroli                   
#>   AH95775 | Ensembl 104 EnsDb for Mus musculus                 
#>   AH95778 | Ensembl 104 EnsDb for Mus pahari                   
#>   AH95779 | Ensembl 104 EnsDb for Mus spicilegus               
#>   ...       ...                                                
#>   AH95790 | Ensembl 104 EnsDb for Neogobius melanostomus       
#>   AH95825 | Ensembl 104 EnsDb for Periophthalmus magnuspinnatus
#>   AH95836 | Ensembl 104 EnsDb for Prolemur simus               
#>   AH95861 | Ensembl 104 EnsDb for Scophthalmus maximus         
#>   AH95879 | Ensembl 104 EnsDb for Ursus maritimus

mm10 or GRCm38

query(ah, c("mus", 109, "ensdb"))
#> AnnotationHub with 27 records
#> # snapshotDate(): 2025-04-08
#> # $dataprovider: Ensembl
#> # $species: Mus musculus, Ursus maritimus, Scophthalmus maximus, Prolemur si...
#> # $rdataclass: EnsDb
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH109509"]]' 
#> 
#>              title                                              
#>   AH109509 | Ensembl 109 EnsDb for Balaenoptera musculus        
#>   AH109626 | Ensembl 109 EnsDb for Mus caroli                   
#>   AH109640 | Ensembl 109 EnsDb for Mus musculus                 
#>   AH109641 | Ensembl 109 EnsDb for Mus musculus                 
#>   AH109642 | Ensembl 109 EnsDb for Mus musculus                 
#>   ...        ...                                                
#>   AH109671 | Ensembl 109 EnsDb for Neogobius melanostomus       
#>   AH109709 | Ensembl 109 EnsDb for Periophthalmus magnuspinnatus
#>   AH109721 | Ensembl 109 EnsDb for Prolemur simus               
#>   AH109750 | Ensembl 109 EnsDb for Scophthalmus maximus         
#>   AH109783 | Ensembl 109 EnsDb for Ursus maritimus

sessionInfo() 
#> R version 4.5.1 (2025-06-13)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] ensembldb_2.32.0        AnnotationFilter_1.32.0 GenomicFeatures_1.60.0 
#>  [4] AnnotationDbi_1.70.0    Biobase_2.68.0          rtracklayer_1.68.0     
#>  [7] GenomicRanges_1.60.0    GenomeInfoDb_1.44.0     IRanges_2.42.0         
#> [10] S4Vectors_0.46.0        SeedMatchR_2.0.0        AnnotationHub_3.16.0   
#> [13] BiocFileCache_2.16.0    dbplyr_2.5.0            BiocGenerics_0.54.0    
#> [16] generics_0.1.4         
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_1.2.1            dplyr_1.1.4                
#>  [3] blob_1.2.4                  filelock_1.0.3             
#>  [5] Biostrings_2.76.0           bitops_1.0-9               
#>  [7] fastmap_1.2.0               lazyeval_0.2.2             
#>  [9] RCurl_1.98-1.17             GenomicAlignments_1.44.0   
#> [11] XML_3.99-0.18               digest_0.6.37              
#> [13] mime_0.13                   lifecycle_1.0.4            
#> [15] ProtGenerics_1.40.0         KEGGREST_1.48.1            
#> [17] RSQLite_2.4.1               magrittr_2.0.3             
#> [19] compiler_4.5.1              rlang_1.1.6                
#> [21] sass_0.4.10                 tools_4.5.1                
#> [23] yaml_2.3.10                 knitr_1.50                 
#> [25] S4Arrays_1.8.1              htmlwidgets_1.6.4          
#> [27] bit_4.6.0                   curl_6.4.0                 
#> [29] DelayedArray_0.34.1         abind_1.4-8                
#> [31] BiocParallel_1.42.1         withr_3.0.2                
#> [33] purrr_1.1.0                 desc_1.4.3                 
#> [35] grid_4.5.1                  SummarizedExperiment_1.38.1
#> [37] cli_3.6.5                   rmarkdown_2.29             
#> [39] crayon_1.5.3                ragg_1.4.0                 
#> [41] httr_1.4.7                  rjson_0.2.23               
#> [43] DBI_1.2.3                   cachem_1.1.0               
#> [45] parallel_4.5.1              BiocManager_1.30.26        
#> [47] XVector_0.48.0              restfulr_0.0.16            
#> [49] matrixStats_1.5.0           vctrs_0.6.5                
#> [51] Matrix_1.7-3                jsonlite_2.0.0             
#> [53] bit64_4.6.0-1               systemfonts_1.2.3          
#> [55] jquerylib_0.1.4             glue_1.8.0                 
#> [57] pkgdown_2.1.3               codetools_0.2-20           
#> [59] BiocVersion_3.21.1          BiocIO_1.18.0              
#> [61] UCSC.utils_1.4.0            tibble_3.3.0               
#> [63] pillar_1.11.0               rappdirs_0.3.3             
#> [65] htmltools_0.5.8.1           GenomeInfoDbData_1.2.14    
#> [67] R6_2.6.1                    textshaping_1.0.1          
#> [69] lattice_0.22-7              evaluate_1.0.4             
#> [71] png_0.1-8                   Rsamtools_2.24.0           
#> [73] memoise_2.0.1               bslib_0.9.0                
#> [75] SparseArray_1.8.0           xfun_0.52                  
#> [77] fs_1.6.6                    MatrixGenerics_1.20.0      
#> [79] pkgconfig_2.0.3

Tareian Cazares

Introduction

Current Annotation Options

Functions for working with annotations and building transcriptomes for queries

Load data for Rnor7

How annotations were retrieved

Selecting GTF

Selecting .2bit DNA sequences

Code for querying AnnotationHub for references

Hg38

.2bit

ensembldb

version 110 for GRCh38.p13

Version 80 for GRCh38.p2

Rat

.2bit

Rnor6

Rnor7

ensembldb

Rnor6

Rnor7

Mouse

.2bit

mm39 or GCRm39

mm10 or GRCm38

ensembldb

mm39 or GRCm39

mm10 or GRCm38

Selecting `.2bit` DNA sequences

Code for querying `AnnotationHub` for references

`.2bit`

`ensembldb`

`.2bit`

`ensembldb`

`.2bit`

`ensembldb`