genesbynonnuclearlocation: Find genes that are encoded in a specified region of the...

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

Find genes that are encoded in a specified region of the non-nuclear genome. The Plasmodium plastid (apicoplast) genome contains two inverted repeats (IR-A and IR-B), and was deposited to EMBL and GenBank in two halves; the IR-A half (X95275) and the IR-B half (X95276). Note that the mitochondrial sequence is 5967 bps long, the IR-A half of the plastid genome is 15421 bps long and the IR-B half of the plastid genome is 14009 bps long.<br><br> <p>The apicoplast genome of <i>T. gondii</i> RH (Type I) strain is 34996 bps long (GeneBank accession #: <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NC_001799">NC_001799</a>). Click <a href="http://roos.bio.upenn.edu/%7Erooslab/jkissing/plastidmap.html">here</a> to view a map of the <i>T. gondii</i> apicoplast. <p> The genome of the <i>T. gondii</i> mitochondrion has not been sequenced.<br><br>

Arguments

organism	Organism Provide one or more values. Use comma as a delimter.
nonnuclearSequence	Nonnuclear genomic sequence for Plasmodium is from P. falciparum and includes the sequence of the mitochondrial and apicoplast genomes. Provide one or more values. Use comma as a delimter.
start_point	Select the distance (in nucleotides) to the start
end_point	Select the nucleotide you would like to end in. Note that 0 equals the end so you can get genes right up to the end of the sequence. The default settings start = 1 and end = 0 will give you results from the entire sequence.
o-fields	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
o-tables	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
.convert	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and TRUE, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is FALSE, the value from the Web server is returned as is.
.url	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
.json	a logical value controlling whether to use the JSON or the XML version of the method

Value

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duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.