Alternative for Symap

Question

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Is there any alternative tool for Symap?

I want to generate the Whole Genome Dot Plot using two samples.

Answer 1

[Philipp Bayer]

Symap runs Nucmer/Promer from Mummer internally, so you may be able to use these directly: http://mummer.sourceforge.net/

You can also try LASTZ if you have only one sequence to align.

Answer 2

[Erik Wright]

You can create whole genome dot plots in R with the DECIPHER package. On this page there is an example of how they look. The steps are to (1) create a sequence database, (2) find the syntenic regions, and (3) make the dot plot. Starting from each genome in a separate FASTA file, the process would look like:

library(DECIPHER)

# connect to an in-memory database
db <- dbConnect(SQLite(), ":memory:")

# load the sequences from each FASTA file
Seqs2DB("<<PATH TO GENOME 1>>", "FASTA", db, "Genome1")
Seqs2DB("<<PATH TO GENOME 2>>", "FASTA", db, "Genome2")

# find the syntenic regions and plot them
synteny <- FindSynteny(db)
pairs(synteny) # create a dot plot

dbDisconnect(db)

The process can be extended to more than two genomes as desired. Hope that helps!