emboss-test 6.4.0-2 / usr / share / EMBOSS / test / memtest.dat

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abiview = abiview ../../data/abiview.abi -graph cps -auto
acdc = acdc embossversion -auto
antigenic = antigenic tsw:opsd_human -auto
backtranseq = backtranseq tsw:opsd_human -auto
banana = banana tembl:x65923 -graph ps -auto
banana-graphps = banana tembl:x65923 -graph ps -auto
banana-graphcps = banana tembl:x65923 -graph cps -auto
banana-graphpng = banana tembl:x65923 -graph png -auto
cai = cai tembl:x65923 -auto
chaos = chaos tembl:x65923 -graph ps -auto
charge = charge tsw:opsd_human -auto
checktrans = checktrans ../../data/paamir.pep -auto
chips = chips tembl:x65923 -auto
cirdna = cirdna -infile ../../data/data.cirp -graph ps -auto
codcmp = codcmp -first Eecoli.cut -second Ehaein.cut -auto
coderet = coderet tembl:x65923 -auto
compseq = compseq tsw:opsd_human -auto
cons = cons ../../data/globins.msf -auto
cpgplot = cpgplot tembl:x65923 -graph ps -auto
cpgreport = cpgreport tembl:x65923 -auto
cusp = cusp tembl:x65923 -auto
cutgextract = cutgextract ../../data -auto
cutseq = cutseq tembl:x65923 -from 20 -to 500 -auto
dan = dan tembl:x65923 -auto
#
seqret-dbblast-entry = seqret qapblast:CO9_FUGRU -out x.x -auto
seqret-dbblast-acc = seqret qapblast-acc:Q90515 -out x.x -auto
seqret-dbblast-query = seqret qapblast:n* -out x.x -auto
seqret-dbblast-all = seqret qapblast:* -out x.x -auto
seqret-dbfasta-entry = seqret qanfasta:m11903 -out x.x -auto
seqret-dbfasta-acc = seqret qanfasta-acc:Z46957 -out x.x -auto
seqret-dbfasta-query = seqret qanfasta:m* -out x.x -auto
seqret-dbfasta-all = seqret qanfasta:* -out x.x -auto
seqret-dbflat-entry = seqret qanflat:m11903 -out x.x -auto
seqret-dbflat-acc = seqret qanflat-acc:Z46957 -out x.x -auto
seqret-dbflat-acc2 = seqret tembl-acc:V00451 -out x.x -auto
seqret-dbflat-query = seqret qanflat:m* -out x.x -auto
seqret-dbflat-key = seqret tembl-key:a* -out x.x -auto
seqret-dbflat-all = seqret qanflat:* -out x.x -auto
seqret-dbgcg-entry = seqret qangcg:X65923 -out x.x -auto
seqret-dbgcg-acc = seqret qangcg-acc:Z46957 -out x.x -auto
seqret-dbgcgpir-des = seqret qapirall-des:cytochrome -out x.x -auto
seqret-dbgcg-query = seqret qangcg:m* -out x.x -auto
seqret-dbgcg-all = seqret qangcg:* -out x.x -auto
seqret-dbgcgpir-des = seqret qapirall-des:cytochrome -out x.x -auto
#
#seqret-xdbblast-entry = seqret qapblast:CO9_FUGRU -out x.x -auto
#seqret-xdbblast-acc = seqret qapblast-acc:Q90515 -out x.x -auto
#seqret-xdbblast-query = seqret qapblast:n* -out x.x -auto
#seqret-xdbblast-all = seqret qapblast:* -out x.x -auto
seqret-xdbfasta-entry = seqret qanxfasta:m11903 -out x.x -auto
seqret-xdbfasta-acc = seqret qanxfasta-acc:Z46957 -out x.x -auto
seqret-xdbfasta-query = seqret qanxfasta:m* -out x.x -auto
seqret-xdbfasta-all = seqret qanxfasta:* -out x.x -auto
seqret-xdbflat-entry = seqret qanxflat:m11903 -out x.x -auto
seqret-xdbflat-acc = seqret qanxflat-acc:Z46957 -out x.x -auto
seqret-xdbflat-query = seqret qanxflat:m* -out x.x -auto
seqret-xdbflat-key = seqret qanxflatall-key:a* -out x.x -auto
seqret-xdbflat-all = seqret qanxflat:* -out x.x -auto
seqret-xdbgcg-entry = seqret qanxgcg:X65923 -out x.x -auto
seqret-xdbgcg-acc = seqret qanxgcg-acc:Z46957 -out x.x -auto
seqret-xdbgcgpir-des = seqret qaxpirall-des:cytochrome -out x.x -auto
seqret-xdbgcg-query = seqret qanxgcg:m* -out x.x -auto
seqret-xdbgcg-all = seqret qanxgcg:* -out x.x -auto
seqret-xdbgcgpir-des = seqret qaxpirall-des:cytochrome -out x.x -auto
#
dbiblast = dbiblast -dir ../../wormpep -file wormpep -index . -db worm -auto
dbiblast-mem = dbiblast -nosystemsort -dir ../../wormpep -file wormpep -index . -db worm -auto
dbiblast-swnew = dbiblast -dir ../../data -db swnew -auto
dbiblast-list = dbiblast -dir ../../data -file 'swsplit.00.pin,swsplit.01.pin,swsplit.02.pin,swsplit.03.pin,swsplit.04.pin' -index . -db swsplit -auto
dbiblast-wild = dbiblast -dir ../../data -file swsplit.*.pin -index . -db swsplit -auto
dbiblast-wildstar = dbiblast -dir ../../data -file swsplit.*.* -index . -db swsplit -auto
dbifasta = dbifasta -dir ../../wormpep -file wormpep -index . -id idacc -db worm -auto
dbifasta-mem = dbifasta -dir ../../wormpep -file wormpep -index . -id idacc -db worm -nosystemsort -auto
dbiflat = dbiflat -dir ../../swiss -file seq.dat -index . -id swiss -db swiss -auto
dbiflat-mem = dbiflat -dir ../../swiss -file seq.dat -index . -id swiss -db swiss -nosystemsort -auto
dbigcg = dbigcg -dir ../../embl -file '*.seq' -index . -id embl -db embl -auto
dbigcg-mem = dbigcg -nosystemsort -dir ../../embl -file '*.seq' -index . -id embl -db embl -auto
dbigcg-2 = dbigcg -dir ../../pir -file '*.seq' -index . -id pir -db pir -auto
dbigcg-mem2 = dbigcg -nosystemsort -dir ../../pir -file '*.seq' -index . -id pir -db pir -auto
#dbxblast =test= dbxblast -dir ../../wormpep -file wormpep -index .  -id idacc -dbres worm -db worm -auto
#dbxblast-list =test= dbxblast -dir ../../data -file 'swsplit.00.pin,swsplit.01.pin,swsplit.02.pin,swsplit.03.pin,swsplit.04.pin' -index . -dbres swissresource -dbname swsplit -auto
#dbxblast-wild =test= dbxblast -dir ../../data -file swsplit.*.pin -index . -dbres swissresource -dbname swsplit -auto
#dbxblast-wildstar =test= dbxblast -dir ../../data -file swsplit.*.* -index . -dbres swissresource -dbname swsplit -auto
dbxfasta = dbxfasta -dir ../../wormpep -file wormpep -index . -id idacc -dbres swissresource -dbname worm -auto
dbxflat = dbxflat -dir ../../swiss -file seq.dat -index . -id swiss -dbres swissresource -dbname swiss -auto
dbxgcg = dbxgcg -dir ../../embl -file '*.seq' -index . -id embl -dbres emblresource -dbname embl -auto
dbxgcg-2 = dbxgcg -dir ../../pir -file '*.seq' -index . -id pir -dbres pirresource -dbname pir -auto
dbxgcg-3 = dbxgcg -dir ../../pir -file '*.seq' -index . -id pir -dbres pirresource -dbname pir -fields "id,acc,des,key,org" -auto
#
degapseq = degapseq ../../data/globins.msf -auto
descseq = descseq -desc 'Test' tsw:opsd_human -auto
diffseq = diffseq tembl:x65923 tembl:x65921 -auto
distmat = distmat ../../data/globins.msf -auto
dotmatcher = dotmatcher tembl:x65923 tembl:x65921 -graph ps -auto
dotpath = dotpath tembl:x65923 tembl:x65921 -graph ps -auto
dottup = dottup tembl:x65923 tembl:x65921 -graph ps -auto
dreg = dreg tembl:x65923 -pattern ggcaggcgcgc -auto
einverted = einverted tembl:d00596 -auto
einverted-wild = einverted 'tembl:m*' -auto
seqret-embl1 = seqret -auto tembl:x65923
seqret-emblmany = seqret -auto 'tembl:m*'
embossdata = embossdata -fetch -file Eamino.dat -outfile ./Eamino.dat -auto
embossversion = embossversion -auto
emowse = emowse 'tsw:*takru' ../../data/test.mowse -auto
entrails =test= entrails -auto
entret = entret tembl:x65923 -auto
equicktandem = equicktandem tembl:x65923 -auto
est2genome = est2genome tembl:x65923 tembl:x65921 -auto
est2genome-2 = est2genome tgenbank:x65923 tembl:x65921 -auto
est2genome-3 = est2genome tgenbank-acc:X65923 tembl-acc:X65921 -auto
etandem = etandem tembl:x65923 -auto
extractseq = extractseq tembl:x65923 -region '20-50' -auto
seqretallfeat-1 =test= seqretallfeat -auto tembl:x65923
seqretallfeat-many =test= seqretallfeat -auto 'tembl:m*'
findkm = findkm ../../data/test.findkm -graph ps -auto
freak = freak tembl:x65923 -auto
fuzznuc = fuzznuc tembl:x65923 -patt ggcaggcgcgc -auto
fuzzpro = fuzzpro tsw:opsd_human -patt MMNKQFR -auto
fuzztran = fuzztran tembl:x65923 -patt kat -auto
garnier = garnier tsw:opsd_human -auto
geecee = geecee tembl:x65923 -auto
getorf = getorf tembl:x65923 -auto
hmoment = hmoment tsw:opsd_human -auto
iep = iep tsw:opsd_human -auto
infoalign = infoalign ../../data/globins.msf -auto
infoseq = infoseq tsw:opsd_human
intconv =test= intconv ../../data/data.linp -auto
isochore = isochore tembl:x13776 -graph ps -graph ps -auto
lindna = lindna -infile ../../data/data.linp -graph cps -auto
marscan = marscan tembl:x65923 -auto
maskfeat = maskfeat tembl:x65923 -auto
maskseq = maskseq tembl:x65923 -regions '20-50' -auto
matcher = matcher tembl:x65923 tembl:x65921 -auto
megamerger = megamerger tembl:x65923 tembl:x65921 -auto
merger = merger tembl:x65923 tembl:x65921 -auto
msbar = msbar tembl:x65923 -auto
needle = needle tembl:x65923 tembl:x65921 -auto
newcpgreport = newcpgreport tembl:u23808 -auto
newcpgseek = newcpgseek tembl:u23808 -auto
newseq = newseq -name fred -desc test -type p -seq acdefg -auto
noreturn = noreturn ../../data/oddcomp.comp -auto
notseq = notseq 'tsw:*' -exclude='ops*' -auto
nthseq = nthseq ../../swiss/seq.dat -num 5 -auto
octanol = octanol tsw:opsd_human -graph ps -auto
oddcomp = oddcomp 'tsw:*' -infile ../../data/oddcomp.comp -auto
palindrome = palindrome tembl:x65921 -min 4 -auto
pasteseq = pasteseq tembl:x65923 tembl:x65921 -pos 200 -auto
patmatdb = patmatdb 'tsw:*' -motif kat -auto
patmatmotifs = patmatmotifs tsw:opsd_human -auto
#patmattest =test= patmattest tsw:opsd_human -expr kat -auto
pepcoil = pepcoil tsw:opsd_human -auto
pepnet = pepnet tsw:opsd_human -graph ps -auto
pepstats = pepstats tsw:opsd_human -auto
pepwheel = pepwheel tsw:opsd_human -graph ps -auto
pepwindow = pepwindow tsw:opsd_human -graph ps -auto
pepwindowall = pepwindowall tsw:opsd_human -graph ps -auto
plotcon = plotcon ../../data/globins.msf -graph ps -auto
plotorf = plotorf 'tembl:x65923' -graph ps -auto
polydot = polydot 'tembl:m*' -graph ps -auto
preg = preg 'tsw:*' -pattern kat -auto
prettyplot = prettyplot ../../data/globins.msf -graph ps -auto
prettyseq = prettyseq tembl:x65923 -auto
prima =test= prima tembl:x65923 -auto
primersearch = primersearch 'tembl:*' ../../data/primers -auto
profit = profit ../../data/globins.prophecy tsw:hba_human -auto
prophecy = prophecy ../../data/globins.msf -type g -auto
prophet = prophet tsw:hba_human ../../data/prophecy.gribskov -auto
recoder = recoder tembl:x65923 -sbeg 31 -send 50 -auto
remap = remap -notran -sbeg 1 -send 60 tembl:j01636 -enzymes 'taqi,bsu6i,acii,bsski' -auto
remap-tran = remap -sbeg 1 -send 60 tembl:j01636 -enzymes 'taqi,bsu6i,acii,bsski' -auto
restover = restover tembl:x65923 -seqcomp acgt -auto
restrict = restrict tembl:x65923 -auto
revseq = revseq tembl:x65923 -auto
seealso = seealso fuzznuc -outfile fuzznuc.isee
seqinfo =test= seqinfo tsw:opsd_human -auto
seqmatchall = seqmatchall 'tembl:x65923*' -auto
seqret = seqret tsw:opsd_human -auto
seqretall =test= seqretall 'tembl:x65923*' -auto
seqretallfeat =test= seqretallfeat 'tembl:x65923*' -auto
seqret-feat = seqret -feat tembl:x65923 -auto
seqretset =test= seqretset ../../data/globins.msf -auto
seqretsplit = seqretsplit 'tembl:x65923*' -auto
seqretset-1 =test= seqretset -auto tsw:opsd_human
seqretset-many =test= seqretset -auto 'tsw:opsd_*'
showalign = showalign ../../data/globins.msf -auto
showdb = showdb
showfeat = showfeat tembl:x65923 -auto
showorf = showorf tembl:x65923 -auto
showseq = showseq tembl:x65923 -auto
shuffleseq = shuffleseq tembl:x65923 -auto
sigcleave = sigcleave tsw:opsd_human -auto
silent = silent tembl:x65923 -sbeg 31 -send 50 -auto
sixpack = sixpack -sbeg 1 -send 60 tembl:j01636  -auto
splitter = splitter -size 500 tembl:x65923 -auto
stretcher = stretcher tembl:x65923 tembl:x65921 -auto
stretcher-coffee = stretcher tsw:opsd_human tsw:opsd_xenla -aform tcoffee -auto
supermatcher = supermatcher tembl:x65923 tembl:x65921 -auto
syco = syco -plot tembl:x65923 -cfile Echicken.cut -graph ps -auto
textsearch = textsearch 'tsw:*' opsin -auto
tfm = tfm tfm -nomore
tmap = tmap tsw:opsd_human -graph ps -auto
transeq = transeq -frame r tembl:x65923 -auto
trimseq = trimseq tembl:x65923 -window 20 -percent 10 -auto
vectorstrip = vectorstrip tembl:x65923 -vectors ../../data/data.vectorstrip -auto
water = water tsw:opsd_human tsw:opsd_xenla -auto
whichdb = whichdb x65921 -auto
whichdb-none = whichdb notfound -auto
wobble = wobble tembl:x65923 -graph ps -auto
wordcount = wordcount tembl:x65923 -auto
wordmatch = wordmatch tembl:x65923 tembl:x65921 -word 10 -auto
wossname = wossname -search codon -auto
#
# EMBASSY Packages
# ================
#
# DOMAINATRIX
# -----------
#
#contacts = contacts -cpdb ../../data -cpdbextn .pxyz -con ../../data -conextn .con -thresh 1.0 -vdwf Evdw.dat -conlogf contacts.log
domainer = domainer -scop ../../qa/scopparse-keep/all.scop -ccfp ../../qa/pdbplus-keep/ -ccfoutdir .  -pdboutdir .  -cpdblogf domainer.log1 -pdblogf domainer.log2 -auto
# requires a modified stamp package installed to run scopalign
#scopalign = scopalign -scopf ../../data/structure/all.scop2 -path ../../data
# broken. ACD changed. How to specify now? Wait for qatest example
###siggen = siggen -algpath ../../data -algextn .align -conpath ../../data -conextn .con -sparsity 10 -randomize N -datafile EBLOSUM62 -scoreseq Y -scorencon Y -scoreccon Y -scoreboth N -postsim Y -auto
#swissparse = swissparse -keyfile ../../data/test.terms -spfile ../../data/test.seq -auto
#
# TOPO
# ----
#
topo = topo tsw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr -basic=db -ohaa=da -araa=dg -graph ps -sections="18 35 49 67 94 115 136 156 165 184 211 232" -nomembrane -sigrange="74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa"

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