hi there,

I have got a very large sequence, in which I have to move every 500bp a time and do some processing there.

I read that Bio::Location::Simple could help to define the start and the end position. but I would like to continue the walk through out the length of the sequence.

is there any effective way of doing this in simple perl?
thanks



Potentially, yes.   How is the sequences stored?  Is it in a file where you need to move forward 500 bytes at a time?     If so, you can use seek to move to a new location in the file and read to read a certain number of bytes.

Yes, it is  stored in a file. the sequence are around  30432563 basepairs long.

bioperl has may many modules and methods, I would think there would be one already written to do what you want, but you can certainly try reading the line in 500 byte chunks and process as desired. read() is the function you want to look at.

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