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seqRFLP (version 1.0.1)

Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

Description

This package includes functions for handling DNA sequences, especially simulated RFLP and TRFLP pattern based on selected restriction enzyme and DNA sequences.

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Version

Install

install.packages('seqRFLP')

Monthly Downloads

24

Version

1.0.1

License

GPL-2

Maintainer

Qiong Ding

Last Published

October 29th, 2012

Functions in seqRFLP (1.0.1)

ConvFas

Convert files to fasta format
dataframe2fas

Convert dataframe to fasta format
seqRFLP-package

Simulation and visualization of Restriction Fragment Length Polymorphism(RFLP) pattern from DNA sequences
selEnz

Selecting restriction enzyme
clipprobe

Finding the sequences that could be clipped given two primers.
read.phy

Read phylip file
findprobe

Find probes matching sites
plotenz

Plotting the simulated RFLP or TRFLP pattern
file.cat

Copy or concatenate files to one.
enzCut

Restriction enzyme cutting pattern
enzdata

The restriction enzyme datasets.
fil.phy

Internal phylip format data
gnames.fas

Get the names of sequences from fasta objects.
raw2Fas

Read and converting raw DNA files to fasta format.
read.nxs

Read nexus file
as.fasta

Coerce "phy" or "nex" objects to fasta format.
revComp

Reverse complement sequence
read.fasta

Read fasta file
fil.fas

Fasta data example.
fil.nxs

Internal nexus data.
rename.fas

Change the sequence names of fasta objects.
write.fasta

Write fasta format object to file
frag.dat

Reports for simulated RFLP cutting pattern