StockholmMultipleAlignment-class: StockholmMultipleAlignment objects

In brendanf/inferrnal: Interface to Call Programs from Infernal RNA Covariance Model Package

StockholmMultipleAlignment objects

Description

The StockholmMultipleAlignment class contains a multiple sequence alignment along with its annotations, as defined for the Stockholm file format.

Usage

StockholmDNAMultipleAlignment(
  x = character(),
  start = NA,
  end = NA,
  width = NA,
  use.names = TRUE,
  rowmask = NULL,
  colmask = NULL,
  GF = character(),
  GS = list(),
  GR = list(),
  GC = character()
)

StockholmRNAMultipleAlignment(
  x = character(),
  start = NA,
  end = NA,
  width = NA,
  use.names = TRUE,
  rowmask = NULL,
  colmask = NULL,
  GF = character(),
  GS = list(),
  GR = list(),
  GC = character()
)

StockholmAAMultipleAlignment(
  x = character(),
  start = NA,
  end = NA,
  width = NA,
  use.names = TRUE,
  rowmask = NULL,
  colmask = NULL,
  GF = character(),
  GS = list(),
  GR = list(),
  GC = character()
)

Arguments

x	(character vector, aligned XStringSet or MultipleAlignment of an appropriate type) multiple sequence alignment without Stockholm extensions
start, end, width, use.names, rowmask, colmask	passed to the appropriate MultipleAlignment constructor, unless "x" is already a MultipleAlignment
GF	(named character vector or BStringSet) Free-text annotations which belong to the alignment file as a whole. The name of each element is a tag identifying the type of data. (See Details).
GS	(named list of named character vectors or BStringSetList) Free-text annotations which belong to the individual sequences in the alignment. The names of the outer list or BStringSetList are tags identifying the type of data for each element. (See Details). Names of inner character vectors or BStringSets match the names of sequences in the alignment, but there is no requirement that every sequence must be annotated for every tag.
GR	(named list of named character vectors or BStringSetList) Annotations for individual residues in the alignment. The names of the outer list or BStringSetList are tags identifying the type of data for each element. (See Details). Names of inner character vectors or BStringSets match the names of sequences in the alignment, but there is no requirement that every sequence must be annotated for every tag. Unlike GS tags, the width of all elements must be the same, and must match the width of the alignment.
GC	(named character vector or BStringSet) Annotations which belong to each column of the alignment as a whole. The name of each element is a tag identifying the type of data. (See Details). Unlike GF tags, the width of all elements must be the same, and must match the width of the alignment.

Details

Although the StockholmMultipleAlignment class is agnostic about the specific tags used, the following tags are the most likely to be recognized by Infernal or other software which reads or writes Stockholm files:

Type	Tag	Description
GF	ID	IDentifier
GF	AC	ACcession
GF	DE	DEscription
GF	AU	AUthor
GF	GA	GAthering threshold
GF	NC	Noise Cutoff
GF	TC	Trusted Cutoff
GS	WT	WeighT
GS	AC	ACcession number
GS	DE	DEscription
GS	DR	Database Reference
GS	OS	OrganiSm (species)
GS	OC	Organism Classification (clade, etc.)
GS	LO	Look (Color, etc.)
GR	SS	Secondary Structure
GR	SA	Surface Accessibility
GR	TM	TransMembrane
GR	PP	Posterior Probability
GR	LI	LIgand binding
GR	AS	Active Site
GR	pAS	AS - Pfam predicted
GR	sAS	AS - from SwissProt
GR	IN	INtron (in or after)
GC	RF	ReFerence
GC	SS_cons	Secondary Structure consensus
GC	SA_cons	Surface Accessibility consensus
GC	TM_cons	TransMembrane consensus
GC	PP_cons	Posterior Probability consensus
GC	LI_cons	LIgand binding consensus
GC	AS_cons	Active Site consensus
GC	pAS_cons	AS - Pfam predicted consensus
GC	sAS_cons	AS - from SwissProt consensus
GC	IN_cons	INtron (in or after) consensus

Value

a new StockholmMultipleAlignment object

Slots

GF

BStringSet. Free-text annotations which belong to the alignment file as a whole. The name of each element is a tag identifying the type of data. (See Details).

GS

BStringSetList. Free-text annotations which belong to the individual sequences in the alignment. The name of each BStringSet is a tag identifying the type of data. (See Details). Names of individual BString elements match the names of sequences in the alignment, but there is no requirement that every sequence must be annotated for every tag.

GR

BStringSetList. Annotations for individual residues in the alignment. The name of each BStringSet is a tag identifying the type of data. (See Details). Names of individual BString elements match the names of sequences in the alignment, but there is no requirement that every sequence must be annotated for every tag. Unlike GS tags, the width of all elements must be the same, and must match the width of the alignment.

GC

BStringSet. Annotations which belong to each column of the alignment as a whole. The name of each element is a tag identifying the type of data. (See Details). Unlike GF tags, the width of all elements must be the same, and must match the width of the alignment.

Examples

# Typically a StockholmMultipleAlignment object is read from a file created
# by other software, but it can also be created manually.
# This example reproduces the example file given in the Stockholm format
# definition.
samp <- StockholmAAMultipleAlignment(
    x = c(
        "O83071/192-246" = "MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS",
        "O83071/259-312" = "MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY",
        "O31698/18-71"   = "MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS",
        "O31698/88-139"  = "EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE",
        "O31699/88-139"  = "EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE"
    ),
    GF = c(
        ID = "CBS",
        AC = "PF00571",
        AU = "Bateman A",
        CC = paste("CBS domains are small intracellular modules mostly",
                   "found in 2 or four copies within a protein."),
        SQ = "67"
    ),
    GS = list(
        # ACcession number
        AC = c(
            "O31698/18-71" = "O31698",
            "O83071/192-246" = "O83071",
            "O83071/259-312" = "O83071",
            "O31698/88-139" = "O31698"
        ),
        # OrganiSm
        OS = c("O31698/88-139" = "Bacillus subtilis")
    ),
    GR = list(
        # Surface Accessibility
        SA = c(
            "O83071/192-246" = "999887756453524252..55152525....36463774777"
        ),
        # Secondary Structure
        SS = c(
            "O83071/259-312" = "CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE",
            "O31698/18-71"   = "CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH",
            "O31698/88-139"  = "CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH"
        ),
        # Active Site
        AS = c(
            "O31699/88-139"  = "________________*__________________________"
        ),
        # INtron
        IN = c(
            "O31699/88-139"  = "____________1______________2__________0____"
        )
    ),
    GC = c(
        # Secondary Structure consensus
        SS_cons = "CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH"
    )
 )
 samp

brendanf/inferrnal documentation built on Sept. 30, 2024, 6:40 a.m.