genesbyphyleticprofile: Find genes that have a homology-based phylogenetic profile...

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

Description

Find P.f. and P.y. genes that have a homology-based phylogenetic profile similar to a specified list of genes. This search also allows you to determine how similar in terms of phylogenetic profile the members of the query list are as they will hit more of the same genes the more similar the members of the query list are to one another. <br><br>

The phylogenetic profile (homology-based) of a gene is a series of 164 "present" or "absent" calls reflecting the presence or absence of a putative homolog in 164 completely sequenced genomes. Similarity between profiles is a good indicator of functional linkages between proteins (see Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 1999 96, 4285-4288). Data on ORFs with the most similar profiles to a given query ORF is also available, and can be used to establish the function of uncharacterized ORFs, based on the similarity of their profiles (see Date SV & Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnology 2003 21:1055-1062) with ORFs of known function.

Arguments

ds_gene_ids	input a comma delimited set of gene ids, or upload a file
signature	Used to pass the Users Signature to the component sites
min_mutual_information_score	Enter the minimum mutual information score to report similarities. The score range is from 0.472 to 1.67
include_only_queries	Click yes to to restrict the results returned to only those genes which have been input as query ids. This allows you to determine the relatedness of your query set
min_num_query_matches	Enter the minimum number of queries you want to match to your genes. If you input 5 genes ids for your query and enter 5 minimum number of queries then the only genes returned would be ones that all 5 queries match
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.