genesbyestoverlap: Find genes with evidence of expression based on expressed...

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

Description

Find genes with evidence of expression based on expressed sequence tags (ESTs). For example: What <i>P. falciparum</i> genes overlap with aligned ESTs from the 3D7 gametocyte library?<p> EST overlap with an annotated gene is a useful way to verify gene predictions but the absense of overlapping ESTs does not mean that a gene is not expressed. Showing the advanced parameters allows you to specify more or less stringent alignment and overlap parameters.

Arguments

libraryIdGenes	Select a clone library. Provide one or more values. Use comma as a delimter.
max_number_best_alignments	EST sequences can have two (or more) best alignments that have the same percent identity, length and score. This parameter allows you to specify the maximum number of these best alignments that will be considered for any EST to be included in the query. For example, if you specify 1 then all the ESTs that do not have a unique best alignment will be ignored in the query.
min_number_est_aligned	Enter the minimum number of ESTs that must align from the libraries selected to return a gene.
bp_overlap_gte	Overlap of expressed sequence tag (EST) alignments with annotated genes is a useful approach to verify gene predictions. In general, the specificity of this evidence is proportional to the overlap length.
best_alignment_only	Select yes to return only those EST alignments that are the best alignment for the EST. Many of the ESTs align at multiple positions in the genome. Selecting yes will consider only those alignments that are the best for each EST
high_confidence_only	Select yes to return only those EST alignments that are consistent. We define define consistent as having >= 95% identity (the majority have >= 99%) and aligning the EST sequence in a manner that is consistent with a gene model. Ie, there can be gaps (representing introns) in the target genomic sequence but not in the EST query.
min_percent_identity	You can specify a minimum percent identity of the alignment between the EST and genomic DNA. We only store alignments with >= 90% identity
min_percent_est_aligned	Enter the minimum percentage of bases in the EST sequence that are aligned to genomic DNA in this alignment.
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.