[Bioc-sig-seq] How to graphical represent different views on a reference genomic sequence

Purnachander purna at atc.tcs.com
Tue Aug 4 09:03:27 CEST 2009


Dear all,

I've loaded a complete genome into variable "mychr" and created many 
views of it.
How can I represent all the generated views in a graphical plot?

" mychr" is :
  1860725-letter "DNAString" instance
seq: 
TGGTACCGGAAGCTATGCGTTAAAAAAGGAATAATG...GCAATTACCGGTAACGAAAAATTTCATGCGCCTTTC

Views generated are :
views:
        start     end width
  [1]    2231   11434  9204 
[GAGGTATGGAAACCTGATCTAGCC...TTCACCATAGTCGATTATAACAC]
  [2]   11784   18426  6643 
[GTCACATCCGGGATTTTGCTCTGG...CCTTTTCTTCGTTGAGAAATTTC]
    ...     ...     ...   ... ...
[366] 1851121 1856489  5369 
[GAAGTGGTAACCTCTGATCCTTCA...CATCATCATGAAGTCGAACGGAT]
[367] 1858686 1860020  1335 
[TTCAAATGTTCGTAATACTTTTCA...ACGAATCTTGCCAACCTCATAGT]

How can I graphically represent these views on a reference genome?

Regards,
Purna



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