Also worth mentioning the makeTxDbFrom*() functions from the GenomicFeatures package.

For example makeTxDbFromUCSC() lets you choose your table/track:

library(GenomicFeatures)
supportedUCSCtables("susScr11")
#     tablename         track subtrack
# 1     refGene  RefSeq Genes     <NA>
# 2 xenoRefGene  Other RefSeq     <NA>
# 3     ensGene Ensembl Genes     <NA>
# 4     genscan Genscan Genes     <NA>

txdb <- makeTxDbFromUCSC("susScr11", "ensGene")
txdb
# TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: susScr11
# Organism: Sus scrofa
# Taxonomy ID: 9823
# UCSC Table: ensGene
# UCSC Track: Ensembl Genes
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Ensembl gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 49448
# exon_nrow: 262635
# cds_nrow: 219938
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2019-11-13 15:03:05 -0800 (Wed, 13 Nov 2019)
# GenomicFeatures version at creation time: 1.38.0
# RSQLite version at creation time: 2.1.2
# DBSCHEMAVERSION: 1.2

See ?makeTxDbFromUCSC for more information.

Or use makeTxDbFromEnsembl() if you prefer to fetch the gene models directly from Ensembl:

txdb <- makeTxDbFromEnsembl("Sus scrofa")
txdb
# TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: Ensembl
# Organism: Sus scrofa
# Ensembl release: 98
# Ensembl database: sus_scrofa_core_98_111
# MySQL server: ensembldb.ensembl.org
# transcript_nrow: 63041
# exon_nrow: 319126
# cds_nrow: 550324
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2019-11-13 15:09:34 -0800 (Wed, 13 Nov 2019)
# GenomicFeatures version at creation time: 1.38.0
# RSQLite version at creation time: 2.1.2
# DBSCHEMAVERSION: 1.2

See ?makeTxDbFromEnsembl for more information.

Finally note that AnnotationHub hosts a few EnsDb objects which are functionally equivalent to TxDb objects with some additional capabilities:

library(AnnotationHub)
hub <- AnnotationHub()
z <- query(hub, c("sus scrofa", "ensdb"))
z
# AnnotationHub with 12 records
## snapshotDate(): 2019-10-29 
## $dataprovider: Ensembl
## $species: Sus scrofa
## $rdataclass: EnsDb
## additional mcols(): taxonomyid, genome, description,
##   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
##   rdatapath, sourceurl, sourcetype 
## retrieve records with, e.g., 'object[["AH53243"]]' 
#
#            title                          
#  AH53243 | Ensembl 87 EnsDb for Sus Scrofa
#  AH53747 | Ensembl 88 EnsDb for Sus Scrofa
#  AH56713 | Ensembl 89 EnsDb for Sus Scrofa
#  AH57796 | Ensembl 90 EnsDb for Sus Scrofa
#  AH60819 | Ensembl 91 EnsDb for Sus Scrofa
#  ...       ...                            
#  AH64991 | Ensembl 94 EnsDb for Sus scrofa
#  AH68020 | Ensembl 95 EnsDb for Sus scrofa
#  AH69274 | Ensembl 96 EnsDb for Sus scrofa
#  AH73969 | Ensembl 97 EnsDb for Sus scrofa
#  AH75101 | Ensembl 98 EnsDb for Sus scrofa

ensdb <- hub[["AH75101"]]
ensdb
# EnsDb for Ensembl:
# |Backend: SQLite
# |Db type: EnsDb
# |Type of Gene ID: Ensembl Gene ID
# |Supporting package: ensembldb
# |Db created by: ensembldb package from Bioconductor
# |script_version: 0.3.4
# |Creation time: Mon Sep 30 23:25:30 2019
# |ensembl_version: 98
# |ensembl_host: localhost
# |Organism: Sus scrofa
# |taxonomy_id: 9823
# |genome_build: Sscrofa11.1
# |DBSCHEMAVERSION: 2.1
# | No. of genes: 31907.
# | No. of transcripts: 63041.
# |Protein data available.

See documentation in the ensembldb package for more information.

Best,

H.

Hi Julie, Thank you very much for your quick response. The problem has been resolved by following the script from James and Hervé. I will try several sequences following the vignettes for the design. Thanks again, Xin