removing ALUs and Vector sequences from text sequence files

Rifat Hamoudi rifat at icr.ac.uk
Sun Jan 26 12:04:02 EST 1997


Hi,
	I used VEP and REP to remove vector and ALU repeat sequences 
from the sequence text files. I would like to clarify a few points.

Does VEP remove vector sequence for you? It seems to create a file 
with extension corresponding to vector name and the original file 
have nothing in it. How can one remove partial vector sequence?

REP creates a filename with extension .ALU, when I look at the 
contents of that file I found it to be the same as the original 
except for a head indicating a number e.g. 5 100. Does this mean that 
sequence 5 to 100 is ALU and should be ignored? Is there anyway using
Staden software, that I can remove ALU sequences from text files 
automatically? If so how?

Thanks.


Rifat.

rifat at icr.ac.uk







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