[Bioperl-l] Genbank/EMBL output

[Keith James]

>>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:

    Matthew> Hi, Are these the same? I would have thought that:

    Matthew> complement(join(1..50,60..100))

    Matthew> is equivalent to:

    Matthew> join(complement(60..100),complement(1..50))

    Matthew> or do the operators join & complement not work how I
    Matthew> thought?

Looking at the feature table definition:

complement(location)
    Find the complement of the presented sequence in
    the span specified by "location" (i.e., read the complement of the
    presented strand in its 5'-to-3' direction)

join(location,location, ... location)
    The indicated elements should be
    joined (placed end-to-end) to form one contiguous sequence

[...]

complement(join(2691..4571,4918..5163))
    Joins regions 2691 to 4571 and 4918 to 5163, then 
    complements the joined segments (the feature is 
    on the strand complementary to the presented strand)

join(complement(4918..5163),complement(2691..4571))
    Complements regions 4918 to 5163 and 2691 to 4571, then 
    joins the complemented segments (the feature is 
    on the strand complementary to the presented strand)

If I've read this correctly then

      e1  e2
  5' ACT GGT
     TGA CCA 5'

complement(join(e1,e2))             -> ACCAGT

join(complement(e2),complement(e1)  -> ACCAGT

join(complement(e1),complement(e2)  -> AGTACC

Unless I've misunderstood too...

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -