Question: Is there a maximum length in EMBOSS needle?
gravatar for xien0114
17 months ago by
xien01140 wrote:

I install BioPython and EMBOSS in my Ubuntu, and it works normally when I input 2 sequences (length <= 4000)

But I create new sequences (length = 10000) and test it, the error occurred.

Bio.Application.ApplicationError: Non-zero return code 1 from 'needle -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5', message 'Needleman-Wunsch global alignment of two sequences'

Is this occurred because of its length? If then how can I break this limit?

alignment • 429 views
ADD COMMENTlink written 17 months ago by xien01140

A true Needleman Wunsch implementation like needle needs memory proportional to the product of the sequence lengths. For two sequences of length 10,000,000 and 1,000 it therefore needs memory proportional to 10,000,000,000 characters. Two arrays of this size are produced, one of ints and one of floats so multiply that figure by 8 to get the memory usage in bytes. That doesn't include other overheads. Therefore only use water and needle for accurate alignment of reasonably short sequences.

If you run out of memory, try using stretcher instead.

ADD REPLYlink written 17 months ago by Pierre Lindenbaum132k

Check that you don't have any error in your command/code (maybe show it). Another possibility is you may be running out of memory.

ADD REPLYlink written 17 months ago by Jean-Karim Heriche24k
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