finding LINEs in flax

[leogg23]

Hi,

I am trying to characterize some LINE insertions and wanted to find
out if anyone knows about a program or method to clearly define the
limits of this element. Most programs either give you similarity to an
element without really allowing you to set the edge of the element
with the host sequence. I guess finding target site duplications would
be easiest but I do not see any program that does this...and what if
these have been lost?. Most programs depend on similarity or finding
the structure for full elements, and most LINEs I have are truncated.

thanks for your help

L.

[IntegronBoy]

Dear leogg23,

Sorry for the delay of my reply. Actually I am on an expert on the
LINE elements because, such as most of people of this forum, work on
prokaryotes in which there is no LINE. Neverthess, we are open to
discussion. I think you should ensure that the already known
duplication sites share common features (in term of sequences, %GC, GC
skew, hairpin, ...), but I fear there is so much copy of LINEs in a
genome, some of which likely to have been degenerated after, that you
can't easily fin something. On other hand, if your LINEs are
truncated, they are most likely unfunctional. What is thus the purpose
of your study ? Deciphering the history of the LINE invasion in you
interest genome ??
Good luck anyway
Tom

[FATEME KANI]

hi tom,i was research about prevalence of integron class 1 in my region.

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