Fig 1.
Schematic representation of the annotation process with AGouTI.
Fig 2.
Overview of key features of AGouTI.
(A) The interdependence between genomic and transcriptomic coordinates. (B) The de novo assignment of the region to the intervals overlapping with transcript features. (C) The GTF feature hierarchy as provided by agouti create_db after inspection of the GTF file along with example lists of attributes available for selection during annotation for gene and transcript features.
Table 1.
Comparison of AGouTI features with other similar tools.
Table 2.
Example output of the annotation of the transcriptomic intervals in custom format with AGouTI.
The original columns of the input file (selected from psRNAtarget output for clarity) are marked with grey. The complete versions of the original and annotated tables are available in S1 Text.
Fig 3.
Benchmark results of AGouTI performed on the annotation of the miRNA binding sites in Brassica napus.
(A) Dependence of memory usage and agouti create_db execution time on the number of genes included in processed GTF file. (B) Dependence of memory usage and agouti annotate execution time on the number of intervals provided for annotation. Error bars represent the standard deviation for ten repetitions.