AlignSynteny {DECIPHER} | R Documentation

## Pairwise Aligns Syntenic Blocks

### Description

Performs pairwise alignment of all blocks of synteny between sets of sequences.

### Usage

    AlignSynteny(synteny,
                 dbFile,
                 tblName = "Seqs",
                 identifier = "",
                 processors = 1,
                 verbose = TRUE,
                 ...)

### Arguments

`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`.

### Details

`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.

### Value

A list with elements for each pair of `identifier`s in `synteny`. Each list element contains a `DNAStringSetList` one pairwise alignment per syntenic block.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`FindSynteny`, `Synteny-class`

### Examples

    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

[Package DECIPHER version 2.8.1 Index]