as.fasta

Convert alignment/sequence in matrix/vector format to FASTA object.

 utilities

Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.

Barry Grant

bio3d

Biological Structure Analysis

Xin-Qiu Yao

Lars Skjaerven

Julien Ide

as.fasta function

<dl> <dt>x</dt>
<dd>a sequence character matrix/vector (e.g obtained from
 <code>get.seq</code> or <code>seqbind</code>).</dd> <dt>id</dt>
<dd>a vector of sequence names to serve as sequence
 identifers. By default the function will use the row names of the
 alignment if they exists, otherwise ids will be generated.</dd> <dt>...</dt>
<dd>arguments passed to and from functions.</dd></dl>

Arguments

Author

Alignment to FASTA object — as.fasta

<dl>

 <dt>x</dt>
<dd>a sequence character matrix/vector (e.g obtained from
 <code>get.seq</code> or <code>seqbind</code>).</dd>

 <dt>id</dt>
<dd>a vector of sequence names to serve as sequence
 identifers. By default the function will use the row names of the
 alignment if they exists, otherwise ids will be generated.</dd>

 <dt>...</dt>
<dd>arguments passed to and from functions.</dd>

</dl>

as.fasta: Alignment to FASTA object

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples