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An inverted repeat (IR) consists of two arms (or stems) of similar DNA or RNA—with one inverted and complemented relative to the other—adjacent to a central, usually nonhomologous, spacer sequence. Smaller IRs stems are typically found in mRNA sequences where they create stem-loop or hairpin structures as the complementary stems form base pairs. Larger IRs are found in genomic sequences and IRs are also found at the boundaries of transposable elements.
This program detects approximate inverted repeats. It can be tuned, using the parameters, to target different stem lengths, different spacer lengths, and different degrees of approximation. It allows GT pairing, which occurs in RNA stem-loops. It also allows detection of mirror repeats (where the stems are inverted, but not complemented). This is useful for establishing background occurrence for statistical analysis of IRs.
In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. The repeat table, viewable in a web browser, contains information about each repeat, including its location, size, and nucleotide content. Clicking on the location indices in one of the table entries opens a second browser page that shows an alignment of the stems to each other. Sequence information sent to the server is confidential and deleted after program execution.
This material is based upon work supported by the National Science Foundation under Grant No. DBI-0413462
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Last revised July 5, 2023
Send any questions or comments to: Gary Benson |