output from test script

embassytestOutput.txt (text/plain), 6.85 KB, created by Jeffrey Gardner (RETIRED) on 2006-11-04 15:25:12 UTC

 [32;01m*[0m EMBOSS version (from "embossversion"): 4.0.0

 [32;01m*[0m Use "seqret" to store a sequence in GenBank format, in lowercase.
 [32;01m*[0m Add a title using "descseq" and convert to Fasta format. Print it
 [32;01m*[0m on screen in EMBL format.

ID   PhiKZ-ORF144 standard; DNA; UNC; 783 BP.
DE   Putative endolysin, complete CDA
SQ   Sequence 783 BP; 254 A; 146 C; 151 G; 232 T; 0 other;
     atgaaagtat tacgcaaagg cgataggggt gatgaggtat gtcaactcca gacactctta        60
     aatttatgtg gctatgatgt tggaaagcca gatggtattt ttggaaataa cacctttaat       120
     caggtagtta aatttcaaaa agataattgt ctagatagtg atggtattgt aggtaagaat       180
     acttgggctg aattattcag taaatattct ccacctattc cttataaaac tatccctatg       240
     ccaactgcaa ataaatcacg tgcagctgca actccagtta tgaatgcagt agaaaatgct       300
     actggcgttc gtagccagtt gctactaaca tttgcttcta ttgaatcagc attcgattac       360
     gaaataaaag ctaagacttc atcagctact ggttggttcc aattccttac tggaacatgg       420
     aaaacaatga ttgaaaatta tggcatgaag tatggcgtac ttactgatcc aactggggca       480
     ttacgtaaag atccacgtat aagtgcttta atgggtgccg aactaattaa agagaatatg       540
     aatattcttc gtcctgtcct taaacgtgaa ccaactgata ctgatcttta tttagctcac       600
     ttctttgggc ctggtgcagc ccgtcgtttc ctgaccactg gccagaatga attagctgct       660
     acccatttcc caaaagaagc tcaggcaaac ccatctattt tttataacaa agatgggtca       720
     cctaaaacca ttcaagaagt ttataactta atggatggta aagttgcagc acatagaaaa       780
     taa                                                                     783
//

 [32;01m*[0m Search for common restriction sites (using "restrict" and the Rebase
 [32;01m*[0m database). We expect to find only a few since viral DNA has evolved to
 [32;01m*[0m protect itself from restriction enzymes. (There is only one hit, for
 [32;01m*[0m the EcoRII enzyme, starting at 610.)

########################################
# Program: restrict
# Rundate: Sat Nov 04 2006 17:23:45
# Commandline: restrict
#    -auto
#    -enzymes BamHI, EcoRI, EcoRII
#    -sitelen 4
#    [-sequence] phikz-lys.fasta
#    [-outfile] stdout
# Report_format: table
# Report_file: stdout
########################################

#=======================================
#
# Sequence: PhiKZ-ORF144     from: 1   to: 783
# HitCount: 1
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2000000000
# Minimum length of recognition site: 4
# Blunt ends allowed
# Sticky ends allowed
# DNA is linear
# Ambiguities allowed
#
#=======================================

  Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
    610     614 EcoRII      CCWGG               609    614         .         .

#---------------------------------------
#---------------------------------------

 [32;01m*[0m Could we mutate the sequence to make the viral DNA even more robust to
 [32;01m*[0m restriction systems whilst keeping the same translation product? This
 [32;01m*[0m is investigated using "recoder". (There are seven possible mutations.)

########################################
# Program: recoder
# Rundate: Sat Nov 04 2006 17:23:45
# Commandline: recoder
#    -auto
#    -enzymes EcoRII
#    [-sequence] phikz-lys.fasta
#    [-outfile] stdout
# Report_format: table
# Report_file: stdout
########################################

#=======================================
#
# Sequence: PhiKZ-ORF144     from: 1   to: 783
# HitCount: 7
#
# KEY:
# Dir: Direction (Rev for reverse complement)
# EnzymeName: Enzyme name
# RS-Pattern: Restriction enzyme recognition site pattern
# Base-Posn: Position of base to be mutated
# AAs: Amino acid. Original sequence(.)After mutation
# Mutation: The base mutation to perform
# 
# Creating silent mutations
#
#=======================================

  Start     End Dir    EnzymeName RS-Pattern Base-Posn    AAs Mutation
    610     614 .      EcoRII     CCWGG            612    P.P     T->G
    610     614 .      EcoRII     CCWGG            612    P.P     T->C
    614     610 Rev    EcoRII     CCWGG            610    R.R     G->A
    614     610 Rev    EcoRII     CCWGG            612    R.R     A->C
    614     610 Rev    EcoRII     CCWGG            613    T.T     C->G
    614     610 Rev    EcoRII     CCWGG            613    T.T     C->A
    614     610 Rev    EcoRII     CCWGG            613    T.T     C->T

#---------------------------------------
#---------------------------------------

 [32;01m*[0m Translate gene to protein sequence. We trim the termination "*"
 [32;01m*[0m character from the end of the translation. We use "transeq". The
 [32;01m*[0m translation product is printed on screen in SwissProt format.

ID   PhiKZ-ORF144_1     STANDARD;      PRT;   260 AA.
DE   Putative endolysin, complete CDA
SQ   SEQUENCE   260 AA;  28816 MW;  BD21361996EBBEAB CRC64;
     MKVLRKGDRG DEVCQLQTLL NLCGYDVGKP DGIFGNNTFN QVVKFQKDNC LDSDGIVGKN
     TWAELFSKYS PPIPYKTIPM PTANKSRAAA TPVMNAVENA TGVRSQLLLT FASIESAFDY
     EIKAKTSSAT GWFQFLTGTW KTMIENYGMK YGVLTDPTGA LRKDPRISAL MGAELIKENM
     NILRPVLKRE PTDTDLYLAH FFGPGAARRF LTTGQNELAA THFPKEAQAN PSIFYNKDGS
     PKTIQEVYNL MDGKVAAHRK
//

 [32;01m*[0m Show a few basic statistics about the protein using "pepstats".
 [32;01m*[0m Molecular weight of the protein is 28814.90 Da (in 260 residues).
 [32;01m*[0m Create an hydropathy plot in PNG format to search for transmembrane
 [32;01m*[0m helices. The PNG graph shows three maxima at around residues 75, 100
 [32;01m*[0m and 135.

PEPSTATS of PhiKZ-ORF144_1 from 1 to 260

Molecular weight = 28814.90  		Residues = 260   
Average Residue Weight  = 110.827 	Charge   = 7.5   
Isoelectric Point = 9.4289
A280 Molar Extinction Coefficient  = 28590   
A280 Extinction Coefficient 1mg/ml = 0.99      
Improbability of expression in inclusion bodies = 0.866

Residue		Number		Mole%		DayhoffStat
A = Ala		23		8.846  		1.029  	
B = Asx		0		0.000  		0.000  	
C = Cys		3		1.154  		0.398  	
D = Asp		14		5.385  		0.979  	
E = Glu		12		4.615  		0.769  	
F = Phe		13		5.000  		1.389  	
G = Gly		20		7.692  		0.916  	
H = His		3		1.154  		0.577  	
I = Ile		12		4.615  		1.026  	
J = ---		0		0.000  		0.000  	
K = Lys		21		8.077  		1.224  	
L = Leu		22		8.462  		1.143  	
M = Met		8		3.077  		1.810  	
N = Asn		16		6.154  		1.431  	
O = ---		0		0.000  		0.000  	
P = Pro		15		5.769  		1.109  	
Q = Gln		9		3.462  		0.888  	
R = Arg		11		4.231  		0.863  	
S = Ser		12		4.615  		0.659  	
T = Thr		21		8.077  		1.324  	
U = ---		0		0.000  		0.000  	
V = Val		13		5.000  		0.758  	
W = Trp		3		1.154  		0.888  	
X = Xaa		0		0.000  		0.000  	
Y = Tyr		9		3.462  		1.018  	
Z = Glx		0		0.000  		0.000  	

Property	Residues		Number		Mole%
Tiny		(A+C+G+S+T)		79		30.385
Small		(A+B+C+D+G+N+P+S+T+V)	137		52.692
Aliphatic	(I+L+V)			47		18.077
Aromatic	(F+H+W+Y)		28		10.769
Non-polar	(A+C+F+G+I+L+M+P+V+W+Y)	141		54.231
Polar		(D+E+H+K+N+Q+R+S+T+Z)	119		45.769
Charged		(B+D+E+H+K+R+Z)		61		23.462
Basic		(H+K+R)			35		13.462
Acidic		(B+D+E+Z)		26		10.000

Created phikz-lys-pep.octanol.1.png