import.msf: Reads a multiple sequence alignment file in MSF format

In bios2mds: From Biological Sequences to Multidimensional Scaling

Description

Reads a Multiple Sequence Alignment (MSA) file in MSF format (.msf extension).

Usage

import.msf(file, aa.to.upper = TRUE, gap.to.dash = TRUE)

Arguments

file	a string of characters to indicate the name of the MSA file to be read.
aa.to.upper	a logical value indicating whether amino acids should be converted to upper case (TRUE) or not (FALSE). Default is TRUE.
gap.to.dash	a logical value indicating whether the dot (.) and tilde (\sim) gap symbols should be converted to the dash (-) character (TRUE) or not (FALSE). Default is TRUE.

Details

Initially, Multiple Sequence Format (MSF) was the multiple sequence alignment format of the Wisconsin Package (WP) or GCG (Genetic Computer Group). This package is a suite of over 130 sequence analysis programs for database searching, secondary structure prediction or sequence alignment. Presently, numerous multiple sequence alignment editors (Jalview and GeneDoc for example) can read and write MSF files.

MSF file displays several specificities:

• a header containing sequence identifiers and characteristics (length, check and weight).

• a separator symbolized by 2 slashes (//).

• sequences of identifiers, displayed by consecutive blocks.

Value

A object of class 'align', which is a named list whose elements correspond to sequences, in the form of character vectors.

Note

import.msf checks the presence of duplicated identifiers in header. Sequences whose identifiers are missing in header are ignored.

Author(s)

Julien Pele

See Also

read.alignment function from seqinr package.
read.GDoc function from aaMI package (archived).

Examples

# reading of the multiple sequence alignment of human GPCRs in MSF format:
aln <- import.msf(system.file("msa/human_gpcr.msf", package = "bios2mds"))

Example output

Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

bios2mds documentation built on April 14, 2020, 5:08 p.m.