AlignSynteny: Pairwise Aligns Syntenic Blocks
In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description Usage Arguments Details Value Author(s) See Also Examples

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 `synteny`.
`identifier`	Optional character string used to narrow the search results to those matching a specific identifier, or an integer sequence corresponding to indices of `rownames(synteny)`. If "" (the default), then all identifiers are selected from `synteny`.
`processors`	The number of processors to use, or `NULL` to automatically detect and use all available processors.
`verbose`	Logical indicating whether to display progress.
`...`	Further arguments to be passed directly to `AlignProfiles`, including `perfectMatch`, `misMatch`, `gapPower`, `terminalGap`, `restrict`, `normPower`, and `substitutionMatrix`.

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 identifiers in synteny. Each list element contains a DNAStringSetList one pairwise alignment per syntenic block.

Erik Wright eswright@pitt.edu

FindSynteny, Synteny-class

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