Web document 3.7. Output of the PRSS program showing an alignment of human beta globin (top sequence) with myoglobin. The myoglobin sequence has been shuffled 100 times, and the resulting Z-score is 210.7 (highlighted).
You can access PRSS and similar programs here:
http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=shuffle
http://www.isrec.isb-sib.ch/experiment/ALIGN_form.html
http://www.ch.embnet.org/software/PRSS_form.html
# /seqprg/bin/prss34_t -p -q -w 80 -m 6 -Z 10000 -A -H -k 100 -f -10 -g -2 @ TMP.q2PRSS evaluates statistical signficance using Smith-Waterman version 34.26 January 12, 2007Please cite: W.R. Pearson (1996) Meth. Enzymol. 266:227-258 @ - QUERY 147 aa vs TMP.q2 - QUERY shuffled sequence 15400 residues in 100 sequences (shuffled) MLE statistics: Lambda= 0.1701; K=0.03061 Smith-Waterman (3.5 Sept 2006) function [BL50 matrix (15:-5)], open/ext: -10/-2 Scan time: 0.030
The best scores are: s-w bits E(10000)QUERY ( 154) 163 45.0 6.3e-06 align
>>>@,
147 aa vs
TMP.q2 library
>>QUERY (154 aa)initn: 163 Z-score: 210.7 bits: 45.0 E(): 6.3e-06
Smith-Waterman score: 163; 25.517% identity (58.621% similar) in 145 aa overlap (4-146:3-147)Entrez Lookup Re-search database General re-search
10 20 30 40 50 60 70 QUERY MVHLTPEEKSAVTALWGKVNVDEVGG--EALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAH
:. : . : .::::..: : :.: ::. .: : . :..: :.. : . .. .: :: :: :.. : .QUERY MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKK 10 20 30 40 50 60 70 80 90 100 110 120 130 140 QUERY LDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
. .. . :.. : : .. . ...... .. :: . .: .:.:..:.. . .: .: QUERY KGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG
80 90 100 110 120 130 140 150 147 residues in 1 query sequences15400 residues in 100 library sequences Tcomplib [34.26] (2 proc) start: Thu Mar 1 07:06:00 2007 done: Thu Mar 1 07:06:00 2007 Scan time: 0.030 Display time: 0.000 Function used was PRSS [version 34.26 January 12, 2007]
# /seqprg/bin/prss34_t -p -q -w 80 -m 6 -Z 10000 -A -H -k 1000 -f -10 -g -2 @ TMP.q2PRSS evaluates statistical signficance using Smith-Waterman version 34.26 January 12, 2007Please cite: W.R. Pearson (1996) Meth. Enzymol. 266:227-258 @ - QUERY 147 aa vs TMP.q2 - QUERY shuffled sequence 154000 residues in 1000 sequences (shuffled) MLE statistics: Lambda= 0.1727; K=0.03112 Smith-Waterman (3.5 Sept 2006) function [BL50 matrix (15:-5)], open/ext: -10/-2 Scan time: 0.240
The best scores are: s-w bits E(10000)QUERY ( 154) 163 45.6 4.2e-06 align
>>>@,
147 aa vs
TMP.q2 library
>>QUERY (154 aa)initn: 163 Z-score: 213.9 bits: 45.6 E(): 4.2e-06
Smith-Waterman score: 163; 25.517% identity (58.621% similar) in 145 aa overlap (4-146:3-147)Entrez Lookup Re-search database General re-search 10 20 30 40 50 60 70 QUERY MVHLTPEEKSAVTALWGKVNVDEVGG--EALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAH
:. : . : .::::..: : :.: ::. .: : . :..: :.. : . .. .: :: :: :.. : .QUERY MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKK 10 20 30 40 50 60 70 80 90 100 110 120 130 140 QUERY LDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
. .. . :.. : : .. . ...... .. :: . .: .:.:..:.. . .: .: QUERY KGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG
80 90 100 110 120 130 140 150 147 residues in 1 query sequences154000 residues in 1000 library sequences Tcomplib [34.26] (2 proc) start: Thu Mar 1 07:07:25 2007 done: Thu Mar 1 07:07:25 2007 Scan time: 0.240 Display time: 0.000 Function used was PRSS [version 34.26 January 12, 2007]