basic {BioSeqClass} | R Documentation

## Assistant Functions

### Description

Assistant functions including read/write files, invoke perl programs, and so on.

### Usage

      ## Elements and groups of base and amino acid
      elements(ele.type)
      aaClass(aa.type)

      pwm(seq,class=elements("aminoacid"))

      .pathPerl(perlName, os)
      .callPerl(perlName, os)

      data(dssp.ss)
      data(aa.index)
      data(PROPERTY)
      data(DiProDB)

### Arguments

`ele.type` | a string for the type of biological sequence. This must be one of the strings "rnaBase", "dnaBase", "aminoacid" or "aminoacid2".
`aa.type` | a string for the group of amino acids. This must be one of the strings "aaH", "aaV", "aaZ", "aaP", "aaF", "aaS" or "aaE".
`seq` | a string vector for the protein or gene sequences.
`class` | a list for the class of biological properties. It can be produced by `elements` and `aaClass`.
`perlName` | a character string for the name of perl program.
`os` | character string, giving the Operating System (family) of the computer.

### Details

`elements` returns a list of basic elements of biological sequence. Parameter "ele.type" supported following selection: "rnaBase" - basic elements of RNA (ATCG). "dnaBase" - basic elements of DNA (AUCG). "aminoacid" - 20 amino acides (RKEDQNWGASTPHYCVLIMF). "aminoacid2" - 20 amino acides and 1 pseudo amino acid "O" (RKEDQNWGASTPHYCVLIMFO). Unknown or uncomplete amino acides will be substituted by pseudo amino acid.

`aaClass` returns a list of amino acids groups depend on their physical-chemical properties. Parameter "aa.type" supports following selection: "aaH" (hydrophobicity): Polar(RKEDQN), Neutral(GASTPHY), Hydrophobic(CVLIMFW) "aaV (normalized Van der Waals volume)": Small(GASCTPD), Medium(NVEQIL), Large(MHKFRYW) "aaZ" (polarizability): Low polarizability (GASDT), Medium polarizability (CPNVEQIL), High polarizability(KMHFRYW) "aaP" (polarity): Low polarity (LIFWCMVY), Neutral polarity (PATGS), High polarity (HQRKNED) "aaF": Acidic (DE), Basic (HKR), Polar (CGNQSTY), Nonpolar (AFILMPVW) "aaS": Acidic (DE), Basic (HKR), Aromatic (FWY), Amide (NQ), Small hydroxyl (ST), Sulfur-containing (CM), Aliphatic (AGPILV) "aaE": Acidic (DE), Basic(HKR), Aromatic (FWY), Amide (NQ), Small hydroxyl (ST), Sulfur-containing (CM), Aliphatic 1 (AGP), Aliphatic 2 (ILV)

`pwm` returns a M*N position weight matrix (PWM) of input sequences. M is the number of elements given by parameter "class". N is the length of each sequence. Each row is a kind of element, and each column is a position. The input sequences must have equal length.

`.pathPerl` write the path of Perl to perl program file.

`.callPerl` invoke Perl program via R.

`dssp.ss` is a vector storing the secondary structure data from DSSP database (http://swift.cmbi.ru.nl/gv/dssp/).

`aa.index` is a list storing the properties of amino acids from AAIndex database (http://www.genome.jp/aaindex).

`PROPERTY` is a list sotring the properties of dinucleotide from B-DNA-VIDEO PROPERTY database (http://wwwmgs.bionet.nsc.ru/mgs/systems/bdnavideo/).

`DiProDB` is a list sotring the conformational and thermodynamic dinucleotide properties from DiProDB database (http://diprodb.fli-leibniz.de/).

### Author(s)

Hong Li

### Examples

      ## amino acids groups depend on their hydrophobicity
      aaClass("aaH")

      ## load data: dssp.ss
      data(dssp.ss)
      ## see the data in dssp.ss
      dssp.ss[1:5]

[Package BioSeqClass version 1.45.0 Index]