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Skipping... %s output Score %4.2f bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try %s -help or read the manual Entrie alignment score contains unseen 'random' score segments You should only use the per-alignments score printed below for the bits score of the alignment Scores as bits over a flat simple random model Scores as bits over a synchronous coding model %s #Gene %d is a pseudo gene - no translation possible GeneWise #Complete Analysis ------------------------------------------------------------- Pfam-SangerPFAMHALFWISEWise2 - database searching mode unreleased$Name: wise2-2-0 $Program: %s version: %s released: %s This program is freely distributed under a Gnu Public License. See -version for more info on copyright Bugs and credits to Ewan Birney ----------------------------------------------------- Algorithm type: GeneWise Search algorithm used: %s Implementation: %s Single genomic vs protein dbProtein db vs genomic dbSingle protein vs genomic dbSearch mode: %s Protein info from: %s Dna info from: %s Comp Matrix: %s Gap open: %d Gap extension: %d Start/End (protein) %s Gene Paras: %s Codon Table: %s Subs error: %2.2g Indel error: %2.2g Model splice? %s Model codon bias? %s Model intron bias? %s Null model %s Alignment Alg %s Starting search...Sorry - could not build gene parameters. Must be a bug of some sortUnable to prepare complexsequenceevalsetString %s was unable to converted into a start/end policy Could not open single dna sequence in %sCould not build a sequence database on %sI could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.Could not read Comparison matrix file in %sCould not get gap string number %sCould not get ext string number %sCould not make %s out as query startCould not make %s out as query endWeird aln number string %s... Weird report stagger asked for %sUnable to set global/local switch on threestatedbCould not read hmm from %s Could not build a threestatemodel database from a single tsm. Weird!Proteins can only have local/global startend policies set, not %sCould not read Protein sequence in %sCould not build ThreeStateModel from a single protein sequence...No protein input file! Yikes!Could not get maximum main_block number %s623623LCould not convert %s to a doubleCannot interpret [%s] as a codon modelling parameter Cannot interpret [%s] as a splice modelling parameter Cannot interpret [%s] as a null model string Cannot interpret [%s] as a intron tieing switch Could not make default random model Could not read a GeneFrequency file in %sCould not read codon table file in %sWCould not open %s as an output file%s (%s) This program is freely distributed under a GPL. See -version for more info Copyright (c) GRL limited: portions of the code are from separate copyrights swisepg in fasta format Options. In any order, '-' as filename (for any input) means stdin Don't use stdin for databases, as on-the-fly indexing is used Protein type [-protein,-prodb,-hmmer,-pfam] [default - protein] Dna type [-dnas,-dnadb] [default - dnadb] Protein [-s,-t,-g,-e,-m] HMM [-hmmer,-hname] Model [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null] Alg [-kbyte,-alg,-aalg,-aln,-noh] Output [-pretty,-genes,-para,-sum,-cdna,-trans,-ace,] ..cont [-gff,-gener,-alb,-pal,-block,-divide] Standard [-help,-version,-silent,-quiet,-errorlog] For more help go %s -help. See WWW help at http://www.sanger.ac.uk/Software/Wise2/ %s Protein input type -protein [default] single protein -prodb protein fasta format db -pfam pfam hmm library -pfam2 pfam old style model directory (2.1) -hmmer single hmmer HMM (version 2 compatible) DNA input type -dnadb [default] dna fasta database -dnas a single dna fasta sequence Protein comparison options -gap [%3d] gap penalty -ext [%3d] extension penalty -matrix [%s] Comparison matrix HMM options -hname For single hmms, use this as the name, not filename Gene Model options -init [%s] [default/global/local/wing/endbias] start-end policy -codon [%s] Codon file -gene [%s] Gene parameter file -subs [%2.2g] Substitution error rate -indel [%2.2g] Insertion/deletion error rate -cfreq [model/flat] Using codon bias or not? [default flat] -splice [model/flat] Using splice model or GT/AG? [default model] -intron [model/tied] Use tied model for introns [default tied] -null [syn/flat] Random Model as synchronous or flat [default syn] -insert [model/flat] Use protein insert model [default flat] Algorithm options -alg [623/2193/] Algorithm used for searching [default 623] -aalg [623/623L/2193/2193L] Algorithm used for alignment [default 623/623L] -cut [%.2f] Bits cutoff for reporting in search algorithm -ecut [n/a] Evalue cutoff for single protein vs DNA searches. -aln [%d] Max number of alignments (even if above cut) -alln [%s] Probability of matching a NNN codon (only for single HMM vs DNAdb) -nohis Don't show histogram on single protein/hmm vs DNA search -report [0] Issue a report every x comparisons (default 0 comparisons) Output options [default -pretty -para] -pretty show pretty ascii output -genes show gene structure -para show parameters -sum show summary output -cdna show cDNA -trans show protein translation -ace ace file gene structure -gff Gene Feature Format file -gener raw gene structure -alb show logical AlnBlock alignment -pal show raw matrix alignment -block [%s] Length of main block in pretty output -divide [%s] divide string for multiple outputs Output for complete analysis (only available for single dna seq vs proteindb) -pseudo Mark genes with frameshifts as pseudogenes -ctrans provide all translations -ccdna provide all cdna -cgene provide all gene structures -cace provide all gene structures in ace format -cdiana provide all gene structures in diana EMBL FT format -cembl provide all gene structures in EMBL FT format -caceh provide all gene structures in halfwise type ace format Jan 1 2008%s Version: %s Released: %s Compiled: %s This program is freely distributed under a Gnu Public License The source code is copyright (c) GRL 1998 and others There is no warranty, implied or otherwise on the performance of this program For more information read the GNULICENSE file in the distribution Credits: Ewan Birney wrote the core code. Portions of this code was from HMMer2, written by Sean Eddy human.gfcodon.tablegapgextematrixmstalncodongenealgaalgcutecutsubsindelallncfreqspliceinitnullintroninsertreportpseudodnasdnadbhmmerpfam2pfamproteinprodbintiehnamenohisprettygffgenesparatranspepcdnasumalbacepalgeneroverdivideblockctranscgenecaceccdnacdianacemblcacehWrong number of arguments (expect 2)! Arg line looked like (after option processing) %s one on one search. Shouldn't you use genewise?Trying to set a evalue cutoff on a non evalue based search. you can only use evalues in a protein HMM vs DNA database search (sorry!)Complete analysis is only available on single dna vs proteindb comparisons - did you use -dnas?Could not build objects!Could not build database-ready objects!Could not search databaseA?⍀Pוҕ⍀P龕蹕⍀P饕蠕⍀P錕臕q⍀qPsn\⍀\PZUG⍀GPA<2⍀2P(#⍀P ⍀P⍀Pݔؔ⍀PĔ返⍀P體覔⍀P钔荔⍀Pyt⍀P`[u⍀uPGB`⍀`P.)K⍀KP6⍀6P!⍀!Pޓ ⍀ Pʓœ⍀P鱓謓⍀P阓蓓⍀Pz⍀Pfa⍀PMH⍀P4/y⍀yPd⍀dPO⍀OP:⍀:PВ˒%⍀%P鷒貒⍀P鞒虒⍀P酒耒⍀Plg⍀PSN⍀P:5⍀P!⍀P}⍀}Ph⍀hP֑ёS⍀SP齑踑>⍀>P餑蟑)⍀)P鋑膑⍀Prm⍀PYT⍀P@;⍀P'"⍀P ⍀P⍀Pܐא⍀PÐ辐l⍀lP骐襐W⍀WP鑐茐B⍀BPxs-⍀-P_Z⍀PFA⍀P-(⍀P⍀P⍀Pݏ⍀Pɏď⍀P鰏諏⍀P闏蒏p⍀pP~y[⍀[Pe`F⍀FPLG1⍀1P3.⍀P⍀P⍀P⍀Pώʎ⍀P鶎豎⍀P靎蘎⍀P鄎⍀Pkft⍀tPRM_⍀_P94J⍀JP 5⍀5P ⍀ P ⍀ PՍЍ⍀P鼍跍⍀P飍融⍀P銍腍⍀Pql⍀PXS⍀P?:x⍀xP&j6jOjhjjjjjjjk0kIkbk{kkkkkkl*lCl\lullllll m$m=mVmommmmmmnn7nPninnnnnnno1oJoco|oooooop+pDp]pvpppppp q%q>qWqpqqqqqqrr8rQrjrrrrr$Ë $Ë$;;;iL.;;;DtL.;;iL.;;;iL.;;$<L.;<L.v;=L.p;h;@iL.];\tL.P;=L.E;=L.:;=L./;=L.$;=L.;=L.;=L.;;hL.:\tL.:H=L.:\tL.:\tL.: <L.:\tL.::`hL.: <L.:L<L.:D<L.z:D<L.o:T<L.d:P<L.Y:L<L.N:D<L.C:H<L.7:|=L.+:l=L. :d=L.:P=L. :T=L.9l=L.9t=L.9X=L.9x=L.9p=L.9=L.9\=L.999DtL.9OhL.c9[9 hL.O9G9gL.;9'9=L.9 9=L.98=L.88gL.8=L.88gL.8=L.8s8gL.k8=L.c8M8gL.E8=L.=8'8gL.8=L.88gL.7=L.77gL.7=L.77gL.7=L.7{7gL.o7=L.e7O7gL.C7t=L.97#7gL.7P=L. 76gL.6X=L.66gL.6T=L.66}gL.6x=L.6s6ygL.g6h=L.]6G6tgL.;6d=L.166pgL.6`=L.65jgL.5|=L.55egL.5p=L.55_gL.5\=L.5k5[gL._5l=L.U5?5TgL.35L=L.)55NgL.54<L.44HgL.4 =L.44BgL.4H<L.44L.22gL.2=L.22fL.2=L.2m2fL.b2<L.S2=2fL.22<L.#2 2fL.2<L.11fL.1<L.11fL.1<L.1}1fL.r1<L.c1M1fL.B1H=L.311fL.18=L.10fL.0$=L.00fL.0=L.00fL.0h<L.s0]0fL.R0<L.C0-0fL."0,=L.0/fL./`<L.//fL./X<L.//fL./p<L./m/fL.b/p<L.S/=/fL.2/<L.#/ /fL./<L...fL..x<L...fL..x<L..}.fL.w._.=L.S.=L.M.H. 7. >.1.p<.).f.#.<..f..h<.. .--@f<---e<---e<--- e<---d<--}-d<-w-h-`d<-\-<<-R- E<-H-E<->-Ld<-8- ,- --T8' --,,,d8',,c8',,@c8',,c8',,b8',r,b8'l,],@b8'W,H,b8'B,3,a8'-,,`a8',=8' ,+ a8'+=8'++`8'++`8'++``8'++ `8'++_8'+s+_8'm+^+h_8'X+I+@_8'C+4+_8'.++^8'+ +^8'+*@^8'**]8'**]8'** ]8'*<8'**\8'*(=8'*t*\8'n*_* \8'O*0=8'I*:*[8'4*%*`[8'**D[8' *)[8'))Z8'))@Z8'))Y8'))Y8'))@Y8')<8'|)m)Y8'])<8'W)H)X8'<)h<8'6)')X8')<8'))@X8'(<8'(((X8'((W8'((W8'((W8'(p<8'((`W8'y(<8's(d(@W8'X(|<8'R(C( W8'=(.(V8'(((V8'((uV8'''@V8'''V8'''U8'''U8'''`U8'''@U8''q' U8'e'<8'_'P'P8'D'<8':' E8'4' ('''Dth%'Th%&&Dth%&Th%&<h%&&Dth%&Th%&&Dth%&@Th%&&Dth%&Th%&r&Dth%h&Sh%b&U&Dth%K&@Sh%E&8&Dth%.&Sh%(&&Dth%&Rh% &%Dth%%Rh%%%Dth%%Qh%%%Dth%%`Qh%%%Dth%%Qh%%%Dth%%Ph%t%<h%j% Eh%d% J%<B%6%.%P"%<%< %%<$P$$P$<$<$$<$$@P$h<$l<$y$h<l$d$PW$ttO$C$;$O/$=!$ =$ $=$K># =##=#5>##O#=#=##=#0>|#=r#h#=^#G>Q#I#@O=#</#<%##<#0>#<""<"5>""O"<"<""<"0>"<"v"<l"5>_"W"NK"<A"7"<-"< ""N"<!!<!<!!N!<!!<!<!!N!8=|!r!8=h!0=[!S!NG!H==!3!H=)!@=!H=! =!!$= N $= N $= H< D< =  $= $= =  = N =u =m c =X =K C N7 =- # = = =  bNL8<<8<t<|<<xn$<_H<ME M68<.8<&0<tt N0<0<(<t<tt|<<0<(<ut<itt[|<M<B<7(<1'(<(<\<d<(<d<d<\<\<d<\<Mx$<d(<\R$<E=M1<&<<<D< M8<8<0<tt0<<~juk$<c0<U0<J@4<80<2%0<0< 4<0<L$<0<0<$<L<Lzp8<d<\8<TJ$<?T<-%L 8<<8<$<P<L<<<<}`Lq,=d(=ZP,=F(=;,=.& Ld< d<`<d<`<K\<\<X<\<X<xKl<bX<N<A9`K-x<#x<|< Kp<@Jp<L<t<p<ttJx<m<e<]S<D<I0<%<< << <I<<<< v<n<f\<MxtA<7)<< <xt< <xt=@IxtskH`xtXxtPFl<6<&<<<< =<===== j@<b@<ZP8<D<8xt,< <==0=<<<=H H0t$=0n_H0S=0M>oH02=0,TH0<0 9H0<0H0<0G0<0G0<0pG0dh<0^OG0C<0=.G0"<0 vG0|<0[G0p<0H<0D<0@G0<0%G0$<0q G0aF0PF0EF0:\t0/\t0)F0=0F0=0`F0 F0E0E0|`E0vg E0[<0Q E0GE0A2D0, DDD<=<=<z=tj<`DT=N=<1<&= < D=<=<D=<=~<tDh=bA<6=0%<D <^D=y<oDc=]L<AP=;1<'D=Ht < T=  < D =  < t=  < Dw =q U UDI <> \=8 . <$ D =  < X=  < D =  < Y h=S I <? 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