I wish to identify genomic repetitive elements from transcriptomic data. Is there any tool which can identify a repetitive element on the basis of its sequence and also consider the expression of that repeat
Dear Mrigaya
Repeat Explorer of Galaxy does the job for you.
Please login to usegalaxy.org
I hope this helps
Prash
Yes, Once you have alligned your RNA-seq reads on genome.
There are repeats sequence libraries on repbase which is http://www.girinst.org/repbase/
or there are repeat masked tables on UCSC (http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=408373381_3zgG711sarzDCL2AFWjIp9f2gFj8&clade=mammal&org=Human&db=hg19&hgta_group=rep&hgta_track=refGene&hgta_table=0&hgta_regionType=genome&hgta_outputType=gff&hgta_outFileName=rmsk.gtf) , just intersect them with your alligned file and get the expression of repeat elements of interest.
you can further normalize them in order to analyze statistically
hth
http://www.girinst.org/repbase/
It is unclear what you mean by complex repeats. The complexity of repeats is a gradient for which you define the boundaries. There are many types of repetitive DNA elements, with very different structural properties and occurrences, from very large, such as inverted Alu sequences and huge palindromes, to very short, such as triplet repeats, from uninterrupted motifs to interrupted repetitive sequences. The degree of interruption is probably something you wish to establish at the outset of your searches. Thus, it seems that it might be useful to define your goals before embarking in large-scale searches. You might also consider the use of control sequences, which you would use to compare the frequencies of whatever motif type(s) you like to investigate. Once the goals are well established, it might be easier to look for appropriate search tools.
Well said Albino. By complex repeats, she probably meant those that are unaligned, not matched and not normalized.
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