STEVE JOHNSON wrote:
>> 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
safe.
Parsnips
--
Aengus Stewart
Scientific Applications Software Support
BBSRC Computing Centre
West Common
Harpenden
Hertfordshire AL5 2JE
UK
Tele: (+44) 1582 762271 ext229
Aengus.Stewart at bbsrc.ac.uk
