Measure dosage of LINE:Maui retrotransposon

camillescott / 2015-fish-dna

Simple genome assembly of an African cichlid

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Measure dosage of LINE:Maui retrotransposon #5

Open ryneches opened 9 years ago

ryneches commented 9 years ago

High abundance kmers align to a Haplochromine instance of a fugu LINE element sequence (GBID AB601475.1). Use relative kmer counts of the LINE element verses the rest of the genome to estimate dosage of this retrotransposon. Compare to other cichlid raw data.

camillescott commented 9 years ago

@ryneches Some papers of interest:

[ ] Review of general repeat finders (including for retrotransposons): http://www.nature.com/hdy/journal/v104/n6/full/hdy2009165a.html
[ ] A k-mer based approach: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0010043
- I'm quite sure we can do better than this
[ ] Another review, more comprehensive:http://bib.oxfordjournals.org/content/8/6/382.full, and the list of software: http://bergmanlab.ls.manchester.ac.uk/?page_id=295

ryneches commented 9 years ago

Also, it turns out that transposons play a major part in egg spot evolution : http://www.nature.com/ncomms/2014/141009/ncomms6149/full/ncomms6149.html

camillescott commented 9 years ago

Also: RepeatMasker

ryneches commented 9 years ago

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap : http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003457