Using the DNA sequence and gene annotation files provided in ENSEMBL web site, the functions implemented in the package try to find the DNA sequences and protein sequences of a list of genomic loci, and to find the genomic coordinates and protein sequences of a list of protein locations, which are the frequent tasks in the analysis of genomic and proteomic data.
The DESCRIPTION file:
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~~ An overview of how to use the package and the most important functions ~~
The package needs three data files. One contains the genetic table, another one contains the DNA sequences of a certain genome, and the third one contains the gene annotations in the same format as the GTF file used in ENSEMBL. The standard genetic table was provided in this package. The other two data files can be downloaded from ENSEMBL web site. For details about those data files and how to obtain them, see the introduction document of this package. Of course you can create your own data files, as long as you observe the format of the files which are specified in the introduction document as well.
The package also needs Perl installed and being available for use in order to run some of the functions.
Once you have the three data files, you need to run the function
generatingCDSaaFile to generate another data file, which
will be used by some of the functions in this package.
Four main functions were implemented in this package so far.
genomicLocToProteinSequence will find the protein
sequences and DNA sequences of the coding regions within a list of genomic
loci given as input.
genomicLocToWholeDNASequence will obtain the
whole DNA sequences of any genomic loci given in the input data.
proteinLocsToGenomic will find the genomic coordinates for a list of
sections in proteins as input.
proteinLocsToProteinSeq will find the
the protein sequences of a list of the protein sections.
Maintainer: Yaoyong Li<email@example.com>
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