/usr/share/wise/wise.per is in wise-data 2.4.1-19.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 | ! this is the wise config file
! for you to fool around with Remember ! lines are comments
! and keys should go flush with the left hand margin
!
! All wise.cfg's at the moment should have interactive key
!
interactive
!
! This is the linkfile designation (for searchwise/swise)
!
linkfile wise.links
!
! The next lines show a UNIX style background system
!
queuecommand nice nohup csh
addamperstand
!
!
viewlength 20
!
! view command for pairwise....
viewer more
!
!viewbackground
!
!
!The next two keys give default codon and matrix files
!I'm using here the fact that pairwise/searchwise will open files
!from WISECONFIGDIR if it can't open the file as the straight filename
!
codondefault codon.table
matrixdefault blosum62.bla
!
!
! The next lines give default for all situations gap and ext
! and other parameters
!
gapdefault 1900
extdefault 200
framedefault 2500
frameextdefault 2000
stopdefault 500
!
!The next lines gives default specific for profiles or protein sequences
!I've found these values by rule of thumb. These values will superceed
! the defaults above
!
gap_pro 2200
ext_pro 200
gap_seq 700
ext_seq 70
!
!This gives the number of cells to report in PairWise
!
reportrate 10000
!
!This tells the screen length in PairWise/Opensearch help files
!
screenlength 20
!
!These give help files
!
localhtmlhelp http://www.sanger.ac.uk/~birney/wise/help/
!
! This gives the SRS link and library links
!
srslink http://www.sanger.ac.uk/srs/srsc?
srslibrary +-l+swissprot+-l+embl+-l+swissnew+-l+emnew
!
! This gives the sort of extensions to append to output file
! in searchwise
!
outputappend .out
htmlappend .html
alignhtmlappend _aln.html
alignappend .aln
!
pairmainhelp pairmain.hlp
pairalignhelp pairaln.hlp
confighelp pairconfig.hlp
!
protopmenuhelp buildprofile.hlp
promatrixmenuhelp pwmatrix.hlp
proweightmenuhelp pwweights.hlp
progapmenuhelp pwgap.hlp
!
searchmainhelp searchmain.hlp
searchparahelp searchaln.hlp
searchsubmithelp searchsubmit.hlp
!
!
!
stagger 500
highscore 250
align 50
!
deletecom
!
!
!
hard_linkage
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