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Pileup Terminology

Aengus Stewart aengus.stewart at bbsrc.ac.uk
Wed Jul 10 06:16:58 EST 1996

> I can't seem to find out what the terms Len and Check refer to on the
> output from Pileup. Any help would be appreciated.

Len is the length of the alignment.  This will not necessarily be 
the same as the length of any of your sequences.  In fact the 
length could and often is longer than your longer sequence.  This 
is as a result of Pileup producing the best alignment which may 
mean the insertion of Gap characters or the alignment is offset 
between your 2 sequences ie it does not begin at position 1 in 
both sequences.

Check is the checksum calculated by GCG programs to validate your 
sequences.  It is derived from the composition and postion of the 
residues in the sequence.  If the checksum calculated from your 
sequence is different from the checksum given then GCG knows that 
the sequence has been altered and will not accept it.  Best thing 
to do is test this.  Alter a sequence in a file and do not 
reformat it and then use it with a GCG prog.  If it runs I will 
eat my hat.  As my hat is currently a Sombero I am in for a hefty 
lunch if this works, but I have a sneaking suspicion my bet is 


Aengus Stewart
Scientific Applications Software Support
BBSRC Computing Centre
West Common
Hertfordshire AL5 2JE

Tele: (+44) 1582 762271 ext229

Aengus.Stewart at bbsrc.ac.uk

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