--------------------------- 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......] |