++ pwd + ORIGDIR=/usr/users/0/nigra/maxsegs + PID=7926 + export PID + TMPDIR=/scratch/nigra/7926 + export TMPDIR + mkdir -p /scratch/nigra/7926 + cd /scratch/nigra/7926 + cp /usr/users/0/nigra/maxsegs/f1k.nbrf f1k.nbrf + cp /usr/users/0/nigra/maxsegs/plbo.nbrf plbo.nbrf + /biomed/bin/maxsegs MaxSegs Program PSC MAXSEGS started on July 4,1776 5:00 Welcome to MAXSEGS sub-sequence alignment program. Version: 3.7 (C)opyright 1992 Pittsburgh Supercomputing Center. Research assisted by this software should cite: Ropelewski, Nicholas and Deerfield, 1997, J. SUPERCOMPUTING 11:237-253 This code based on the algorithm developed by: Waterman and Eggert, 1987, J.MOL.BIOL. 197:723-728 MAXSEGS> ECHO MAXSEGS> TITLE Finding kringles in plbo. Finding kringles in plbo. MAXSEGS> SEQUENCE QUERY=f1k.nbrf ***** Using query sequence from : f1k.nbrf MAXSEGS> SEQUENCE LIBRARY=plbo.nbrf ***** Using library sequence from : plbo.nbrf MAXSEGS> SEQUENCE RESULT=f1-k_maxsegs_plbo_pam40.srt ***** Writing results (alignments) to : f1-k_maxsegs_plbo_pam40.srt MAXSEGS> ALPHABET PROTEIN ***** Using "PROTEIN" alphabet MAXSEGS> SCORE PAM40 ***** Using "PAM40" scoring scheme. MAXSEGS> LIMIT NUMBER=6 cutoff=0 ***** Limiting number of sub-alignments retreived to 6 ***** Limiting lower bound (cutoff) of scores to 0 MAXSEGS> SHOW PARAMETERS ARE: ***** Using "PROTEIN" alphabet ***** Using Gap= -1.00, Newgap= -30.00 ***** Using "PAM40" scoring scheme. A R N D C Q E G H I L K A 6 -6 -3 -3 -6 -4 -2 -1 -6 -4 -5 -6 R -6 8 -5 -9 -7 -1 -8 -9 -1 -5 -7 1 N -3 -5 7 2 -9 -3 -1 -2 1 -4 -7 0 D -3 -9 2 7 -12 -2 3 -2 -3 -6 -11 -4 C -6 -7 -9 -12 10 -12 -12 -10 -6 -6 -13 -12 Q -4 -1 -3 -2 -12 8 2 -6 1 -6 -4 -2 E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 G -1 -9 -2 -2 -10 -6 -3 6 -9 -9 -8 -6 H -6 -1 1 -3 -6 1 -4 -9 9 -9 -6 -5 I -4 -5 -4 -6 -6 -6 -5 -9 -9 8 -1 -5 L -5 -7 -7 -11 -13 -4 -8 -8 -6 -1 7 -7 K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 M -4 -4 -7 -10 -12 -3 -8 -9 -9 0 1 -1 F -7 -7 -7 -12 -11 -11 -12 -8 -5 -2 -2 -12 P -1 -3 -5 -6 -7 -2 -4 -5 -3 -8 -6 -5 S 0 -2 0 -3 -2 -4 -3 -1 -5 -6 -8 -3 T 0 -5 -1 -4 -6 -5 -5 -5 -6 -2 -6 -2 W -12 -1 -9 -14 -14 -12 -15 -13 -9 -12 -10 -10 Y -7 -11 -4 -10 -3 -10 -7 -12 -3 -6 -6 -10 V -2 -6 -6 -7 -5 -6 -6 -5 -6 2 -2 -7 B -2 -5 7 7 -10 -1 3 -1 0 -4 -7 -1 Z -1 -2 -1 3 -11 7 7 -3 1 -4 -4 -2 J -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 M F P S T W Y V B Z J A -4 -7 -1 0 0 -12 -7 -2 -2 -1 -1 R -4 -7 -3 -2 -5 -1 -11 -6 -5 -2 -1 N -7 -7 -5 0 -1 -9 -4 -6 7 -1 -1 D -10 -12 -6 -3 -4 -14 -10 -7 7 3 -1 C -12 -11 -7 -2 -6 -14 -3 -5 -10 -11 -1 Q -3 -11 -2 -4 -5 -12 -10 -6 -1 7 -1 E -8 -12 -4 -3 -5 -15 -7 -6 3 7 -1 G -9 -8 -5 -1 -5 -13 -12 -5 -1 -3 -1 H -9 -5 -3 -5 -6 -9 -3 -6 0 1 -1 I 0 -2 -8 -6 -2 -12 -6 2 -4 -4 -1 L 1 -2 -6 -8 -6 -10 -6 -2 -7 -4 -1 K -1 -12 -5 -3 -2 -10 -10 -7 -1 -2 -1 M 11 -4 -8 -5 -3 -12 -10 -1 -7 -4 -1 F -4 9 -10 -6 -7 -3 2 -7 -7 -11 -1 P -8 -10 8 -1 -3 -12 -12 -5 -4 -2 -1 S -5 -6 -1 6 1 -4 -6 -5 0 -3 -1 T -3 -7 -3 1 7 -11 -6 -2 -1 -4 -1 W -12 -3 -12 -4 -11 13 -3 -15 -10 -12 -1 Y -10 2 -12 -6 -6 -3 9 -6 -4 -7 -1 V -1 -7 -5 -5 -2 -15 -6 7 -6 -5 -1 B -7 -7 -4 0 -1 -10 -4 -6 8 2 -1 Z -4 -11 -2 -3 -4 -12 -7 -5 2 8 -1 J -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 MAXSEGS> MATCH ***** 1 Library sequences processed. HISTOGRAM PLOT: X=score, Y=the number of times the score occured 10-| 7-| 6-| 5-| 3-| 3-| 2-| 1-| 1-| 1-| * ---------------------------------------------------------------------- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 0C 601 Scores (xunits= 8.71) 6 alignments were greater than the cutoff value of 0. MAXSEGS> QUIT ***** Exiting MAXSEGS, one moment please. + ls -la total 24 drwxr-xr-x 2 nigra staff 4096 Jul 6 15:07 . drwxr-xr-x 4 nigra users 4096 Jul 6 15:07 .. -rw-r--r-- 1 nigra staff 5201 Jul 6 15:07 f1-k_maxsegs_plbo_pam40.srt -rw-r----- 1 nigra staff 213 Jul 6 15:07 f1k.nbrf -rw-r----- 1 nigra staff 1645 Jul 6 15:07 plbo.nbrf + /biomed/bin/seqsort -program maxsegs -in f1-k_maxsegs_plbo_pam40.srt -out f1-k_maxsegs_plbo_pam40.out -list f1-k_maxsegs_plbo_pam40.lst Program PSC seqsort - Sequence program output file sorter Version: 1.5 (C)opyright 1992, 1997 Pittsburgh Supercomputing Center. + cp f1-k_maxsegs_plbo_pam40.out /usr/users/0/nigra/maxsegs/f1-k_maxsegs_plbo_pam40.out + '[' 0 -eq 0 ']' + echo ' ' + echo 'Successfully copied f1-k_maxsegs_plbo_pam40.out' Successfully copied f1-k_maxsegs_plbo_pam40.out + echo ' ' + cp f1-k_maxsegs_plbo_pam40.lst /usr/users/0/nigra/maxsegs/f1-k_maxsegs_plbo_pam40.lst + '[' 0 -eq 0 ']' + echo ' ' + echo 'Successfully copied f1-k_maxsegs_plbo_pam40.lst' Successfully copied f1-k_maxsegs_plbo_pam40.lst + echo ' ' + cd /usr/users/0/nigra/maxsegs + /bin/rm -rf /scratch/nigra/7926