FASTA program discussion list

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Hi there, I'm gahoo.
File for test:http://dl.dropbox.com/u/1504421/Temp/seq.zip

fasta-36.3.5b will got this result:

# ./lalign36 -m 10 -n at.fasta os.fasta
LALIGN finds non-overlapping local alignments
 version 36.3.5b Oct, 2011(preload8)
Please cite:
 X. Huang and W. Miller (1991) Adv. Appl. Math. 12:373-381

Query: at.fasta
  1>>>AT1G80070.1 1500 bp_Up Chr 1:30116552..30118054 - 1503 nt
Library: os.fasta
     1503 residues in     1 sequences

Statistics: (shuffled [500]) MLE statistics: Lambda= 0.1390;  K=0.06233
 statistics sampled from 1 (1) to 500 sequences
Threshold: E() < 0.2 score: 97
Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (7.2 Nov 2010)
Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
 Scan time:  0.470

>>>AT1G80070.1, 1503 nt vs os.fasta library
; pg_name: lalign36
; pg_ver: 36.3.5b Oct, 2011(preload8)
; pg_argv:  ./lalign36 -m 10 -n at.fasta os.fasta; pg_name_alg: Smith-Waterman
(SSE2, Michael Farrar 2006)
; pg_ver_rel: 7.2 Nov 2010
; pg_matrix: +5/-4 (5:-4)
; pg_open-ext: -12 -4
; mp_extrap: 60000 500
; mp_stats: (shuffled [500]) MLE statistics: Lambda= 0.1390;  K=0.06233
; mp_KS: -0.0000 (N=0) at   0
; mp_Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (7.2 Nov 2010)
; mp_Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
>>LOC_Os05g07050.1 1500 bp_Up Chr 05:3715990..3714488 (reverse complemented)

>>><<<
>>>///

1503 residues in 1 query   sequences
1503 residues in 1 library sequences
 Scomplib [36.3.5b Oct, 2011(preload8)]
 start: Thu Nov 17 20:57:31 2011 done: Thu Nov 17 20:57:32 2011
 Scan time:  0.470 Display time:  0.040

Function used was LALIGN [36.3.5b Oct, 2011(preload8)]


Meanwhile, fasta-35.4.12 have chances to get similar result. Interestingly, 
the
result changes. Sometimes I got the correct results, sometimes not. Why the
result will change?

My operating system is ubuntu server64 10.04 . And I used 
Makefile.linux64_sse2
to  compile the source. Does it matter?