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How do I get my sequences into Pileup?

You need a file that contains the names of all the sequences you want to put into Pileup. If the sequence files are actually in your own directory, and are all in GCG format, your input file can look like this:
--------------------------- File pileup.inp -------------------
w68343.gb_new
x12871.gb_new
hcu31231.gb_vi
hsig487.gb_pr
---------------------------------------------------------------
When pileup asks for the sequences, type '@pileup.inp' in response. Note the '@' symbol before the filename; this tells GCG that the file contains a list of sequences. The filename itself should not start with '@'!

You don't need to have the sequences in your own directory to align them; pileup (and most GCG programs) can fish out sequences from the databases. For example, a valid file of sequence names would be:

----------------------- File hsp.list --------------------------
LOOKUP in: genbank  of: "[SQ-ALL: hsp70*]"

 3 entries  June  3, 1997 16:11 ..

GB_BA:BBHSP60 ! ID: 120c0005
! DEFINITION  B.burgdorferi hsp60 gene for 60kDa heat shock protein.
GB_BA:BBHSPRO ! ID: 130c0005
! DEFINITION  B.burgdorferi dnaK gene for heat-shock protein.
GB_BA:BBOSPAGE ! ID: 480c0005
! DEFINITION  B.burgdorferi OspA gene for outer surface protein A.
-------------------------------------------------------------------
(This file was output by GCG's Lookup program). In this case, the sequences are still in the database, and Pileup will pull out each sequence at the start of its run. It will take a little longer than if the sequences are in your home directory.

Sample pileup session:
helix% pileup

PileUp creates a multiple sequence alignment from a group of related
sequences using progressive, pairwise alignments.  It can also plot a
tree showing the clustering relationships used to create the alignment. 

 PileUp of what sequences ?  @pileup.inp


   1   w68343.gb_new   392 bp
   2   x12871.gb_new   429 bp
   3  hcu31231.gb_vi   308 bp
   4   hsig487.gb_pr   487 bp

 What is the gap creation penalty (* 5.00 *) ?

[....etc......]