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Detecting tandem repeats in genomic sequences

Goals:

In a given set of genomic sequences, detect perfect or imperfect tandem repeats (TRs) which might have evolved away from their anscestral repeated sequence unit - through point mutations and indels, duplications and losses of losses of repeat units and slippage

Why:

Tandem repeats (TRs) of sequence regions complicate many downstream genomic analyses, and knowing regions covered by TRs would help to minimize errors in many analyses.

Input data:

Genomic sequences (protein). Preferred format: fasta

Pipeline:

1. Detect potential TRs with different prediction algorithms.
2. Statistically validate all predictions.
3. For each significant prediction, construct a profile HMM based on inferred alignment of TR units.
4. Refine TR prediction using a circular profile HMM.
5. Statistically validate the final prediction
6. Output TR information if significant in step 5.

Deliverables:

For each sequence, where TRs were detected, we indicate full information on the TR: starting position, alignments of TR units, and significance values for the TR test and maximum likelihood divergence estimate for TR units (Schaper et al. 2012, NAR).
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