AlignSynteny {DECIPHER} | R Documentation |
Performs pairwise alignment of all blocks of synteny between sets of sequences.
AlignSynteny(synteny, dbFile, tblName = "Seqs", identifier = "", processors = 1, verbose = TRUE, ...)
synteny |
An object of class “Synteny”. |
dbFile |
A SQLite connection object or a character string specifying the path to the database file. |
tblName |
Character string specifying the table where the sequences are located that were used to create the object |
identifier |
Optional character string used to narrow the search results to those matching a specific identifier, or an integer sequence corresponding to indices of |
processors |
The number of processors to use, or |
verbose |
Logical indicating whether to display progress. |
... |
Further arguments to be passed directly to |
AlignSynteny
will extract all sequence regions belonging to syntenic blocks in synteny
, and perform pairwise alignment with AlignProfiles
. Hits are used to anchor the alignment such that only the regions between anchors are aligned.
A list with elements for each pair of identifier
s in synteny
. Each list element contains a DNAStringSetList
one pairwise alignment per syntenic block.
Erik Wright eswright@pitt.edu
db <- system.file("extdata", "Influenza.sqlite", package="DECIPHER") synteny <- FindSynteny(db, minScore=50) DNA <- AlignSynteny(synteny, db) names(DNA) DNA[[1]] # the first set of pairwise alignments DNA[[1]][[1]] # the first block of synteny between H9N2 & H5N1 unlist(DNA[[2]]) # a DNAStringSet of synteny between H9N2 & H2N2