FindSynteny: Finds Synteny in a Sequence Database

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Finds syntenic blocks between groups of sequences in a database.

Usage

FindSynteny(dbFile,
            tblName = "Seqs",
            identifier = "",
            useFrames = TRUE,
            alphabet = AA_REDUCED[[1]],
            geneticCode = GENETIC_CODE,
            sepCost = 0,
            gapCost = -0.01,
            shiftCost = 0,
            codingCost = 0,
            maxSep = 2000,
            maxGap = 5000,
            minScore = 30,
            dropScore = -100,
            maskRepeats = TRUE,
            allowOverlap = FALSE,
            storage = 0.5,
            processors = 1,
            verbose = TRUE)

Arguments

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.
identifier	Optional character string used to narrow the search results to those matching a specific identifier. If "" then all identifiers are selected.
useFrames	Logical specifying whether to use 6-frame amino acid translations to help find more distant hits. Using the alphabet is helpful when the genome is largely composed of coding DNA. If FALSE then faster but less sensitive to distant homology.
alphabet	Character vector of amino acid groupings used to reduce the 20 standard amino acids into smaller groups. Alphabet reduction helps to find more distant homologies between sequences. A non-reduced amino acid alphabet can be used by setting alphabet equal to AA_STANDARD.
geneticCode	Either a character vector giving the genetic code to use in translation, or a list containing one genetic code for each identifier. If a list is provided then it must be named by the corresponding identifiers in the database.
sepCost	Cost per nucleotide separation between hits to apply when chaining hits into blocks.
gapCost	Cost for gaps between hits to apply when chaining hits into blocks.
shiftCost	Cost for shifting between different reading frames when chaining reduced amino acid hits into blocks.
codingCost	Cost for switching between coding and non-coding hits when chaining hits into blocks.
maxSep	Maximal separation (in nucleotides) between hits in the same block.
maxGap	The maximum number of gaps between hits in the same block.
minScore	The minimum score required for a chain of hits to become a block. Higher values of minScore are less likely to yield false positives.
dropScore	The change from maximal score required to stop extending blocks.
maskRepeats	Logical specifying whether to “soft” mask repeats when searching for hits.
allowOverlap	Logical specifying whether to permit blocks to overlap on the same sequence.
storage	Excess gigabytes available to store objects so that they do not need to be recomputed in later steps. This should be a number between zero and a (modest) fraction of the available system memory. Note that more than storage gigabytes may be required, but will not be stored for later reuse.
processors	The number of processors to use, or NULL to automatically detect and use all available processors.
verbose	Logical indicating whether to display progress.

Details

Long nucleotide sequences, such as genomes, are often not collinear or may be composed of many smaller segments (e.g., contigs). FindSynteny searches for “hits” between sequences that can be chained into collinear “blocks” of synteny. Hits are defined as k-mer exact nucleotide matches or k-mer matches in a reduced amino acid alphabet (if useFrames is TRUE). Hits are chained into blocks as long as they are: (1) within the same sequence, (2) within maxSep and maxGap distance, and (3) help maintain the score above minScore. Blocks are extended from their first and last hit until their score drops below dropScore from the maximum that was reached. This process results in a set of hits and blocks stored in an object of class “Synteny”.

Value

An object of class “Synteny”.

Note

FindSynteny is intended to be used on sets of sequences with up to ~100 million nucleotides total per identifier. For this reason, better performance can sometimes be achieved by assigning a unique identifier to each chromosome belonging to a large genome.

Author(s)

Erik Wright [e-mail]

See Also

AlignSynteny, Synteny-class

Examples

db <- system.file("extdata", "Influenza.sqlite", package="DECIPHER")
synteny <- FindSynteny(db)
synteny
pairs(synteny) # scatterplot matrix

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: RSQLite

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Time difference of 0.72 secs

         H9N2     H5N1     H2N2     H7N9     H1N1
H9N2   8 seqs 49% hits 34% hits 48% hits 34% hits
H5N1 6 blocks   8 seqs 29% hits 45% hits 39% hits
H2N2 7 blocks 6 blocks   8 seqs 27% hits 35% hits
H7N9 6 blocks 5 blocks 6 blocks   8 seqs 32% hits
H1N1 6 blocks 6 blocks 6 blocks 6 blocks   8 seqs

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.