CDR1as miRNA example

K-miR example: CDR1as / ciRS-7

K-miR · Tutorial

CDR1as is a published miR-7-binding circular RNA (Hansen et al., 2013). This example annotates its selected seven-nucleotide words with complementary human miRNA seeds.

Sequence

The circBase record hsa_circ_0001946 defines a 1,485-nt, positive-strand circular interval at hg19 chrX:139865339–139866824 (zero-based, half-open). Ensembl assembly mapping places it at GRCh38 X:140783175–140784659 (one-based, inclusive). The sequence was retrieved from the Ensembl genomic sequence endpoint. Coordinates, retrieval URL and checksum.

Run

Supply a background FASTA and use a new output directory:

python examples/run_cdr1as_mirna.py --background /path/to/lncRNA.fa --out results/cdr1as_mirna --top-pct 5

The example script streams transcripts rather than creating a dense count matrix. It normalizes canonical counts per transcript, excludes zero-frequency observations for each word, includes the target, and averages tied ranks. It then calls AnnotateMiRNASeeds on words with KRS percentile ≥0.95. Duplicate identifiers are rejected; identical target sequences are excluded from the background.

The script uses the reference-class counting boundary: 1,478 seven-nucleotide windows from the 1,485-nt linearized sequence. It omits the final possible window and does not count junction-spanning windows.

Demo plot

AnnotateMiRNASeeds(source="KRS", plot=True) produces this bar-plot format. Each row identifies a matched miRNA family and its complementary target word; bar length shows the target's KRS percentile score. The demo plots up to 20 matched rows, ordered by percentile. Results depend on the comparison FASTA and selection parameters.

The miR-7-5p seed GGAAGAC matches GTCTTCC (DNA) / GUCUUCC (RNA). The target word occurs 67 times in the included CDR1as sequence.

Exact seed matches nominate compatible miRNAs. They do not establish expression, binding or sponge activity; KRS percentiles are not P values.