ELF`44 (444 @ @ $  J J /lib/ld-linux.so.2GNU%'% "#& $    !2LjO\3Klu|/^t":$\̈܈{| $"DJ+J,<cLRJ\Ll|+)$2̉$t܉RJ7y= $, $L"__gmon_start__libm.so.6libc.so.6strcpyprintf__strtod_internalstdoutungetc__ctype_bgetenv__strtol_internalgetpidfscanffgetspclosefeofmalloc__ctype_toupperpopenstrrchrfprintf__deregister_frame_infofseekstrncmpstrncpyrealloc_IO_getcstrtoksscanfftellstrcmpsprintffclosestderrexitfopen_IO_stdin_used__libc_start_main__register_frame_infofreeGLIBC_2.1GLIBC_2.0ii yii J%JJJJIIIIIIIII I I I I IIIIIIIIIIIIIII I"I#I$J%J&US[ct:k]5|I%I%Ih%Ih%Ih%Ih%Ih %Ih(%Ih0%Ih8p%Ih@`%IhHP%IhP@%IhX0%Ih` %Ihh%Ihp%Ihx%Ih%Ih%Ih%Ih%Ih%Ih%Ih%Ihp%Ih`%IhP%Ih@%Ih0%Ih %Ih%Ih%Jh%Jh1^PTRhh QVhU=(@u8P$@С$@8ut hdIR(@ÉUÍvU希thJhdIÍvUÐUu uju<[+FjUuu uh6UuuEE PhÍvUSM] UEtPRSQhJt&PRSh]ÉUVSuE ]MUtRQPVhRQPhe[^ÐUVSE] utVSPhIP4h5JjSh 5JtVhB5Jce[^UE ÐUEU Hg+P {ÍvUS] SPmu0uuhV5Juhp5JjSP]ÉUWVS}uURVu UR_WWPS|Ãu7VURhV5JURhp5Jzj&WSe[^_ÐUWVSu] }1ҍKMC=u-Vh5J'Wh5JMQh2=g+t;Vh 5JWh5JMQh`5J$MA<{t;Vh5JWh5JMQh`5J$ujEe[^_ÐUuh5JRj[UWVS}j/W+t)1hhCPƃ ~ SWV6?/t./3e[^_UWVSu] hhj1҉R1ǃ;/uSW$Sj/VhWe[^_ÍvUhuu1 P/ÐUVSu] SVh`AhH@"uShhH@I' J[.SVe[^UWVS}h@1ۃ9}u 6hNC9|hRt5JhUdhjZ=D@th~h==@@thh h=4@u h t&hh"=8@u h h=4@t =8@u5<@h@e[^_ÐUÐUWVSM1;u&} MJDP t4t&K}}7M CUJË}Dz uыM <uF}7M7;u|;u}} MJDPu K}}M e[^_ÐU WVS}EEEE0;udM JDP t+KE0M C]UJEDB uՋM < uFE00;u|;uM <-EPMQhS(U؃uMvUJDP tPBM E T JDQ urBM E T JDQ tL}:u<E@ME M| :t#E@ME M| :uEe[^_ÍvUWVSM1;uv} MJDP t4t&K}}7M CUJË}Dz uыM <uF}7M7;u|;u}} M<:t B}e[^_ÐUhhjj8Khhjju,]Sh5Jh5Jtvh! 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SJh S?h% S4h S) h8 ShK Sh8 Sh S h^ Sh{ Sh Sh S h Sh@ Sh Sh S h Sh` Sh Sxh Sm h S_h STh:SIhSS> h:S0h S%hShS h@Sh ShShS h@Sh ShShS h`Sh ShSh S hSth Sih@S^hSS h SEhS:h S/h`S$ hSh S hSh S hShSh ShS h`Sh Sh ShS hShS~h SshSh h SZhSOhSDh S9 hMS+hSS hShMS hSh Sh Sh`S h Sh ShSh S hShSh Sh S} hSohSdh@SYhSN hS@h`S5hS*h S hShSh@ShS h ShShSh,S h Sh`ShShS hShCSyh`SnhSc hSUhSJhS?hS4 h S&h Sh`ShS h ShSh Sh S h` ShMSh Sh S h Sh Sh Sh Sx h Sjh!S_h@!STh!SI h!S;h"S0h!"S%h@"S h"S h"Sh#Sh@#S h!"Sh#Sh#Sh!"S h%$Sh<$ShP$Shn$S h$Sh$Sth$Sih$S^ h %SPh`%SEh%S:h%S/ h &S!h`&Sh&S h&S h 'Sh%ShW'Shk'S hz'Sh'Sh'Sh'S h'Sh'Sh(S~h@(Ss h(Seh(SZh)SOh!)SD h S6h S+]ÐUh5)hE)jjK54@5,@p¡K58@50@V¡KP p¡KP@ h5)hM)jj9K1ҡKB~ÉU WVSM} uEPQEv} uEPQxEhQ)h_)juEhQ)hf)juE1ۃ ;]u11ɡA9UUUU䍴&} u:EUU@DU<4&} u,@EUUʋ=<@AEEA9|xUC;]:hQ)hE)j,jNjUW UWU GGEGGGU@G G$G(} u?1;A}%uhQ)hl)6 C;A|hQ)hy)UA} u@1;A}#uhQ)h)6 C;A|hQ)h)URe[^_UWVS]h)S肿u!Sh)5JjhQhVkh)V01ۃA9}%$8K;tC;|%&G~jj jP+h)j¾uh)h_)j5A1ۃ;A}5h)h)jW赿C;A|19C9|t&Kh)V1ۋA9}#$8K;tC;|9}Dt&h)j谽t(8|t#jj jPؼƒC9|QhV蔼 EQݼE 8t[^_ÍvUWVS]h)S 0u!Sh)5J蜻j襼,g0Qh($Vh)V踼1ۃA9}#$8K;tC;|G~jjP誺 ݜ+8h)jTuh)h_)j5Ar41ۃ;A}6 h)h)jWF  C;A|198,4C9|,Kh)$V裻1ۋA9}#$8K;tC;|9}@t&h)jPt$8|tjjPz ,4C9|ċ0Qh(V8 I0Q聺E 84[^_ÍvUSh)h)jjh)h)j5A h)h)j5AȻC1;A}'vCDB;A|CC C؋]U4WVSEX HMMx)}HM)Mx }@]Eh)h*j,Eh)h_)jMQEh)hf)j}WEE,9}u\]Ѝ&1;A}8t&ut uu t&ut u u ؐe[^_ÐUWVSh@,hR,jj,EEt&h@,hU,jj1ۃM@BC|E [-%s] [-%s <%s>] The command line is missing an integer at its end. %d%c"%s" (from item %d on the command line) is not an integer. The command line is missing a positive integer at its end. is not a positive integer. The command line is missing a non-negative is not a non-negative integer. The command line is missing a floating point number at its end. %lf%cis not a floating point number. The command line is missing a positive floating is not a positive floating point number. The command line is missing a non-negative floating is not a non-negative floating point number. The command line is missing a string of characters at its end PAGERwmore########################### # README FOR MATALIGN-V2A # Copyright 2002--2005 Ting Wang and Gary Stormo May be copied for noncommercial purposes. Author: Ting Wang and Gary Stormo Department of Genetics Washington University in St. Louis Campus Box 8232 St. Louis, MO 63110 stormo@ural.wustl.edu twang@ural.wustl.edu MatrixAligner-v2a ################# # BASIC OPTIONS # -f1 -f2 -t1 -t2 [-h ] [-n ] [-c0 ] [-c1 ] [-g ] [-a ] [-A ] [-CS ] ####################### # GENERAL INFORMATION # Matrix Aligner is a program to compare two positional specific matrices. The precursor of this program is "CompareTwo". Matalign-v2a made several improvements over the previous establishment of the program. Two input PSSMs should be formatted according to consensus output. They can be either count matrices, or frequency matrices. If a frequency matrix is used, a user-defined "total count" is assumed (default = 10). The scoring function between two positions of the two matrices is ALLR statistic. The alignment algorithm can be either "local alignment" or "global alignment". Both options do not allow gaps. The comparison between the two matrices results in the following output: 1) An alignment between two input matrices. 2) An ALLR score of the comparison. In general, the higher the ALLR score, the more similar are the two matrices. 3) A distance score. Distance between A and B is defined as: ALLR(A,A) + ALLR(B,B) - 2xALLR(A,B). In general, the smaller the distance, the more similar are the two matrices. 4) P-value and E-value of the observed ALLR score. These significance values are calculated based on Karlin-Altschul statistics. The meaning of the p-value is, given two random PSSMs, the probability of observing an equal or higher ALLR score. 5) The aligned parts of the two matrices will be merged into one new matrix and printed as output. ######################## # COMMAND LINE OPTIONS # 0) -h: print these directions. 1) Required options -f1 filename "filename" contains the one matrix. -f2 filename "filename" contains the second matrix. -t1 integer: the type of matrix 1. 0 means count matrix, 1 means frequency matrix. -t2 integer: the type of matrix 1. 0 means count matrix, 1 means 2) Alphabet options -a filename: file containing the alphabet and normalization information. Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be be the genomic frequency of the bases; however, if the "-d" option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet). Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the "-CS" option is used, the alphabet is case sensitive so that a total of 52 different characters are possible. POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS: letter letter normalization POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS: letter:complement letter:complement normalization letter:complement normalization:complement's_normalization Example alphabet file 1: A:T C:G Example alphabet file 2: A:T 0.3 C:G 0.2 3) Options for handling the complement of the matrices --- -c0: ignore the complement -c1: compare both orientation (the default option) 4) Algorithm options -n: if a frequency matrix is compared, a total count is assumed. "n" is the user-defined total count. Default is 10. -g: global alignment. Default is local alignment. ########### # Example # (bifrost)[3:11pm]src_v2a 207>>more matrix1 A | 1 0 0 0 0 0 0 C | 0 14 2 0 0 0 9 G | 15 2 14 16 16 16 2 T | 0 0 0 0 0 0 5 (bifrost)[3:23pm]src_v2a 208>>more matrix2 A | 0 0 1 0 1 0 0 C | 3 22 0 0 0 1 15 G | 18 1 23 24 23 23 1 T | 3 1 0 0 0 0 8 (bifrost)[3:23pm]src_v2a 209>>./matalign-v2a -f1 matrix1 -f2 matrix2 -t1 0 -t2 0 -g COMMAND LINE: ./matalign-v2a -f1 matrix1 -f2 matrix2 -t1 0 -t2 0 -g ***** PID: 4450 ***** Algorithm options: Compare both orientations. Global alignment. Matrix 1 type: count matrix Matrix 2 type: count matrix Matrices Alignment: MATRIX: A | 1 0 0 0 0 0 0 C | 0 14 2 0 0 0 9 G | 15 2 14 16 16 16 2 T | 0 0 0 0 0 0 5 Consensus: G C G G G G c MATCH: | | | | | | | MATRIX: A | 0 0 1 0 1 0 0 C | 3 22 0 0 0 1 15 G | 18 1 23 24 23 23 1 T | 3 1 0 0 0 0 8 Comparison scores: ALLR = 8.3894 Distance = 1.9606 E_value = 3.01e-07 P_value = 3.01e-07 NEW MATRIX: number of sequences = 40 width = 7 crude information = 9.7450 (bits) A | 1 0 1 0 1 0 0 C | 3 36 2 0 0 1 24 G | 33 3 37 40 39 39 3 T | 3 1 0 0 0 0 13 Consensus: GCGGGGc init_profiles()profilehspread_matrix()matrixdcodeint_matrix[]int_matrixdouble_matrix[]double_matrixrError in opening file %s read_int_matrix()matrix[]alloc_column()columnfrequencymake_mirror_profile()mirrorComparison scores: ALLR = %.4f Distance = %.4f E_value = %.4g P_value = %.4g Y@score_function()STscoreSTscore[]DP_functionDPDP_function()DP[]trace_back()hsphsp->matchtrace_back_g()free_scores()score[]scoremerge_HSP()new_profileint_matrixdcode9B.??NEW MATRIX: number of sequences = %d width = %d crude information = %.4f (bits) %c |%3d %3d %3d |Consensus: %cMatrices Alignment: MATCH: x%6s|MATRIX: %5d %5c 9B.?ffffff??ffffff?karlin_altschul()smsm[]Error: The lowest score in the substitution matrix must be negative. Error: The highest score in the substitution matrix must be positive. Error: A positive score is impossible with the given substitution matrix and residue composition. Error: Negative probabilities are disallowed. karlin_lambda_K_H()p0P0Error: Probabilities sum to %.5f and will be normalized to 1. Error: Invalid (non-negative) expected score: %#0.21gError: Value for K may be too large due to insufficient iteration. St$?9m4??9B.?h㈵>?find_score_spectrum()spectrumfailed to find a start pt for newton/raphson Newton/Raphson search failed ?ư>????tIdl,@l0@4@x8@@ <@D@LD@`TL@@  ؛A@      ATCGMKRYWSatcgnׁs?(\µ?Af?Af?<,Ԛ?ZӼ?U؟?Ǻ?ea?_vO?St$? ^)?<,Ԛ?QI?`"?qpptts<Yqpptts;Xpporrri]pporrsh[trTvWrXqtrvTrWXqtrWrTvXqtrrWvTXqrsXXXX;vssqqqqvl<6;6i68h68YX][I# lSjI$m kRs4Xl1Ds4lVD1$<|#<}p!/p/!o44FF8z{ mXlzl lV{Sk1D}p&jRD1|o' JRbrˆ҈"2BRbr‰҉"2BR  (Є` y xI܆(ooo^Odd+<:i,x:_y5_s-n-Y=t(;-s$B?- 1!I"_#v%&1234 5" 6< 8U 9o ; = > ? @ A B% C< DU El F G H I N Q+ RE S] Tv V Y o r u' {A |^ { ' D ^ UO  7"vS3;BE<zRY]5k7wsx- #$%&9 "dinit.c/usr/src/bs/BUILD/glibc-2.1.3/csu/gcc2_compiled.int:t(0,1)=r(0,1);0020000000000;0017777777777;char:t(0,2)=r(0,2);0;127;long int:t(0,3)=r(0,1);0020000000000;0017777777777;unsigned int:t(0,4)=r(0,1);0000000000000;0037777777777;long unsigned int:t(0,5)=r(0,1);0000000000000;0037777777777;long long int:t(0,6)=r(0,1);01000000000000000000000;0777777777777777777777;long long unsigned int:t(0,7)=r(0,1);0000000000000;01777777777777777777777;short int:t(0,8)=r(0,8);-32768;32767;short unsigned int:t(0,9)=r(0,9);0;65535;signed char:t(0,10)=r(0,10);-128;127;unsigned char:t(0,11)=r(0,11);0;255;float:t(0,12)=r(0,1);4;0;double:t(0,13)=r(0,1);8;0;long double:t(0,14)=r(0,1);12;0;complex int:t(0,15)=s8real:(0,1),0,32;imag:(0,1),32,32;;complex float:t(0,16)=r(0,16);4;0;complex double:t(0,17)=r(0,17);8;0;complex long double:t(0,18)=r(0,18);12;0;void:t(0,19)=(0,19)../include/libc-symbols.h/usr/src/bs/BUILD/glibc-2.1.3/build-i386-linux/config.h../include/libintl.h../intl/libintl.h../include/features.h../include/sys/cdefs.h../misc/sys/cdefs.h/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66/include/stddef.h../include/locale.h../locale/locale.hlconv:T(10,1)=s48decimal_point:(10,2)=*(0,2),0,32;thousands_sep:(10,2),32,32;\grouping:(10,2),64,32;int_curr_symbol:(10,2),96,32;\currency_symbol:(10,2),128,32;mon_decimal_point:(10,2),160,32;\mon_thousands_sep:(10,2),192,32;mon_grouping:(10,2),224,32;\positive_sign:(10,2),256,32;negative_sign:(10,2),288,32;\int_frac_digits:(0,2),320,8;frac_digits:(0,2),328,8;\p_cs_precedes:(0,2),336,8;p_sep_by_space:(0,2),344,8;\n_cs_precedes:(0,2),352,8;n_sep_by_space:(0,2),360,8;\p_sign_posn:(0,2),368,8;n_sign_posn:(0,2),376,8;;../include/xlocale.h../locale/xlocale.h__locale_struct:T(13,1)=s36__locales:(13,2)=ar(0,1);0;5;(13,3)=*(13,4)=xslocale_data:,0,192;\__ctype_b:(13,5)=*(0,9),192,32;__ctype_tolower:(13,6)=*(0,1),224,32;\__ctype_toupper:(13,6),256,32;;__locale_t:t(13,7)=(13,8)=*(13,1)../sysdeps/unix/sysv/linux/_G_config.h../sysdeps/unix/sysv/linux/bits/types.hsize_t:t(16,1)=(0,4)__u_char:t(15,1)=(0,11)__u_short:t(15,2)=(0,9)__u_int:t(15,3)=(0,4)__u_long:t(15,4)=(0,5)__u_quad_t:t(15,5)=(0,7)__quad_t:t(15,6)=(0,6)__int8_t:t(15,7)=(0,10)__uint8_t:t(15,8)=(0,11)__int16_t:t(15,9)=(0,8)__uint16_t:t(15,10)=(0,9)__int32_t:t(15,11)=(0,1)__uint32_t:t(15,12)=(0,4)__int64_t:t(15,13)=(0,6)__uint64_t:t(15,14)=(0,7)__qaddr_t:t(15,15)=(15,16)=*(15,6)__dev_t:t(15,17)=(15,5)__uid_t:t(15,18)=(15,3)__gid_t:t(15,19)=(15,3)__ino_t:t(15,20)=(15,4)__mode_t:t(15,21)=(15,3)__nlink_t:t(15,22)=(15,3)__off_t:t(15,23)=(0,3)__loff_t:t(15,24)=(15,6)__pid_t:t(15,25)=(0,1)__ssize_t:t(15,26)=(0,1)__rlim_t:t(15,27)=(0,3)__rlim64_t:t(15,28)=(15,6)__id_t:t(15,29)=(15,3)__fsid_t:t(15,30)=(15,31)=s8__val:(15,32)=ar(0,1);0;1;(0,1),0,64;;__daddr_t:t(15,33)=(0,1)__caddr_t:t(15,34)=(10,2)__time_t:t(15,35)=(0,3)__swblk_t:t(15,36)=(0,3)__clock_t:t(15,37)=(0,3)__fd_mask:t(15,38)=(0,5)__fd_set:t(15,39)=(15,40)=s128fds_bits:(15,41)=ar(0,1);0;31;(15,38),0,1024;;__key_t:t(15,42)=(0,1)__ipc_pid_t:t(15,43)=(0,9)__blkcnt_t:t(15,44)=(0,3)__blkcnt64_t:t(15,45)=(15,6)__fsblkcnt_t:t(15,46)=(15,4)__fsblkcnt64_t:t(15,47)=(15,5)__fsfilcnt_t:t(15,48)=(15,4)__fsfilcnt64_t:t(15,49)=(15,5)__ino64_t:t(15,50)=(15,4)__off64_t:t(15,51)=(15,24)__t_scalar_t:t(15,52)=(0,3)__t_uscalar_t:t(15,53)=(0,5)__intptr_t:t(15,54)=(0,1)../linuxthreads/sysdeps/pthread/bits/pthreadtypes.h../sysdeps/unix/sysv/linux/bits/sched.h__sched_param:T(18,1)=s4sched_priority:(0,1),0,32;;_pthread_fastlock:T(17,1)=s8__status:(0,3),0,32;__spinlock:(0,1),32,32;;_pthread_descr:t(17,2)=(17,3)=*(17,4)=xs_pthread_descr_struct:pthread_attr_t:t(17,5)=(17,6)=s36__detachstate:(0,1),0,32;\__schedpolicy:(0,1),32,32;__schedparam:(18,1),64,32;\__inheritsched:(0,1),96,32;__scope:(0,1),128,32;\__guardsize:(16,1),160,32;__stackaddr_set:(0,1),192,32;\__stackaddr:(17,7)=*(0,19),224,32;__stacksize:(16,1),256,32;;pthread_cond_t:t(17,8)=(17,9)=s12__c_lock:(17,1),0,64;\__c_waiting:(17,2),64,32;;pthread_condattr_t:t(17,10)=(17,11)=s4__dummy:(0,1),0,32;;pthread_key_t:t(17,12)=(0,4)pthread_mutex_t:t(17,13)=(17,14)=s24__m_reserved:(0,1),0,32;\__m_count:(0,1),32,32;__m_owner:(17,2),64,32;\__m_kind:(0,1),96,32;__m_lock:(17,1),128,64;;pthread_mutexattr_t:t(17,15)=(17,16)=s4__mutexkind:(0,1),0,32;;pthread_once_t:t(17,17)=(0,1)_pthread_rwlock_t:T(17,18)=s32__rw_lock:(17,1),0,64;__rw_readers:(0,1),64,32;\__rw_writer:(17,2),96,32;__rw_read_waiting:(17,2),128,32;\__rw_write_waiting:(17,2),160,32;__rw_kind:(0,1),192,32;\__rw_pshared:(0,1),224,32;;pthread_rwlock_t:t(17,19)=(17,18)pthread_rwlockattr_t:t(17,20)=(17,21)=s8__lockkind:(0,1),0,32;\__pshared:(0,1),32,32;;pthread_t:t(17,22)=(0,5)wchar_t:t(19,1)=(0,3)wint_t:t(19,2)=(0,4)_G_int16_t:t(14,1)=(0,8)_G_int32_t:t(14,2)=(0,1)_G_uint16_t:t(14,3)=(0,9)_G_uint32_t:t(14,4)=(0,4)_IO_stdin_used:G(0,1)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)01.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.01.symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.got.rel.bss.rel.plt.init.plt.text.fini.rodata.data.eh_frame.ctors.dtors.got.dynamic.bss.stab.stabstr.comment.note# 1((87 ``p?ЄGo^^NTo0c ܆l  u  ~  /<< ``