Jeremy Buhler jbuhlerwustledu Parts of RepeatMasker Programs Smit AFA Hubley R and Green P RepeatMaskerOpen 40 20132015 httpwwwrepeatmaskerorg RMBlast NCBI variant HMMER for comparisons ID: 1045613
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1. Design and Use of RepeatMaskerJeremy Buhlerjbuhler@wustl.edu
2. Parts of RepeatMaskerProgramsSmit AFA, Hubley R, and Green P. “RepeatMasker-Open 4.0.” 2013-2015. http://www.repeatmasker.org/RMBlast (NCBI variant), HMMER for comparisonsDataDfam https://www.dfam.org
3. OverviewSources of repetitive sequence dataHow RepeatMasker finds repeatsIssues and limitations
4. Data SourceUses a library of known repeat seqsSupplied by Dfam (“DNA families DB”)Repeat families in Dfam are carefully curated using multiple alignment tools.
5. Example of arepeat familysummary page from Dfam
6. Repeats are DNA MotifsRepeats occur in multiple instances, so use motif technology to represent themaccgataggtatacgtatca-tttacgatacatcgct-ggtttacgcgtcaattcaggatgcaccggt-tgtttacgtagcaatctaggatacaccgat-ggtttacgtatcaatttaggatac
7. Two kinds of model:consensus and HMM (= weight matrix + gaps)
8. Why Use Motifs for Repeats?Faster to compare one sequence/model to genome than many seqsEven simple motifs, like a consensus sequence, are better than individual instances for discovering new copies of a repeat.
9. Utility of Motif vs Instancesacacgtatagctactggttcaggc334
10. Utility of Motif vs Instancesacacgtatagctactggttcaggcacaggt2
11. Types of Repeats IdentifiedInterspersed (Alu, LINE, MIR, …)Micro- and mini-satellitesNoncoding RNAs (tRNA, rRNA, snoRNA, …)Short tandem + low complexity (agagagag, actactactact, aaaaataataaaa, …)Common artifacts (E. coli, vectors)
12. OverviewSources of repetitive sequence dataHow RepeatMasker finds repeatsIssues and limitations
13. The BasicsUses RMBlast (BLAST-like tool) to compare query to consensus model libraryUses HMMER (vaguely BLAST-like, but with much fancier math) to compare query to HMM library
14. Partial RepeatsRepeatMasker will cheerfully report an incomplete match to a repeat.Detects best-conserved partsSome repeats (retroposons) typically incomplete
15. Nested RepeatsRepeatMasker tries to detect nestingtime
16. Nested RepeatsRepeatMasker tries to detect nestingtime
17. Nested RepeatsRepeatMasker tries to detect nestingtime
18. Nested RepeatsRepeatMasker tries to detect nestingtime(Please don’t ask me how)
19. Nested RepeatsRepeatMasker tries to detect nestingtime(Please don’t ask me how)See the RepeatMasker presentation by Dr. Jessica Storer for details
20. OverviewSources of repetitive sequence dataHow RepeatMasker finds repeatsIssues and limitations
21. Library ChoiceMake sure to use correct libraries for your target species(Commonly used organisms have preselected library lists)Danger: mis-identifications!
22. Incomplete MaskingHighly diverged repeats can be tough to findMight leave ends of a repeat unmaskedIs this really a new feature?(masked)BLAST hit
23. Use the Right ToolTandem repeats and duplicationsDust (short) — Morgulis et al., 2006TRF (long) — Benson et al., 1999RNAtRNAscan-SE, Infernal, …Other repeatsSearch for matches to Dfam (HMMER) and the NCBI nt database (BLAST)Check the “Repeat tools” page on TE Hub
24. Hey, let’s be careful out there!In conclusion…Neal Wellons; https://flic.kr/p/FrUFPX