This is pdfeTeX, Version 3.141592-1.20a-2.2 (Web2C 7.5.3) (format=pdflatex 2005.5.25)  29 MAY 2005 02:00
entering extended mode
**computation.tex
(./computation.tex
LaTeX2e <2003/12/01>
Babel <v3.8d> and hyphenation patterns for american, french, german, ngerman, d
utch, italian, norsk, portuges, spanish, swedish, nohyphenation, loaded.
(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/size10.clo
File: size10.clo 2004/02/16 v1.4f Standard LaTeX file (size option)
)
\c@part=\count79
\c@section=\count80
\c@subsection=\count81
\c@subsubsection=\count82
\c@paragraph=\count83
\c@subparagraph=\count84
\c@figure=\count85
\c@table=\count86
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/amssymb.sty
Package: amssymb 2002/01/22 v2.2d

(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/amsfonts.sty
Package: amsfonts 2001/10/25 v2.2f
\@emptytoks=\toks14
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
(Font)                  U/euf/m/n --> U/euf/b/n on input line 132.
))
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsmath.sty
Package: amsmath 2000/07/18 v2.13 AMS math features
\@mathmargin=\skip43

For additional information on amsmath, use the `?' option.
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amstext.sty
Package: amstext 2000/06/29 v2.01

(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsgen.sty
File: amsgen.sty 1999/11/30 v2.0
\@emptytoks=\toks15
\ex@=\dimen103
))
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsbsy.sty
Package: amsbsy 1999/11/29 v1.2d
\pmbraise@=\dimen104
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsopn.sty
Package: amsopn 1999/12/14 v2.01 operator names
)
\inf@bad=\count87
LaTeX Info: Redefining \frac on input line 211.
\uproot@=\count88
\leftroot@=\count89
LaTeX Info: Redefining \overline on input line 307.
\classnum@=\count90
\DOTSCASE@=\count91
LaTeX Info: Redefining \ldots on input line 379.
LaTeX Info: Redefining \dots on input line 382.
LaTeX Info: Redefining \cdots on input line 467.
\Mathstrutbox@=\box26
\strutbox@=\box27
\big@size=\dimen105
LaTeX Font Info:    Redeclaring font encoding OML on input line 567.
LaTeX Font Info:    Redeclaring font encoding OMS on input line 568.
\macc@depth=\count92
\c@MaxMatrixCols=\count93
\dotsspace@=\muskip10
\c@parentequation=\count94
\dspbrk@lvl=\count95
\tag@help=\toks16
\row@=\count96
\column@=\count97
\maxfields@=\count98
\andhelp@=\toks17
\eqnshift@=\dimen106
\alignsep@=\dimen107
\tagshift@=\dimen108
\tagwidth@=\dimen109
\totwidth@=\dimen110
\lineht@=\dimen111
\@envbody=\toks18
\multlinegap=\skip44
\multlinetaggap=\skip45
\mathdisplay@stack=\toks19
LaTeX Info: Redefining \[ on input line 2666.
LaTeX Info: Redefining \] on input line 2667.
)
(./slide-article-tom.sty
(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/sfonts.def
File: sfonts.def 1998/06/12 v2.2e Standard LaTeX slide font definitions

(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/ot1lcmss.fd
File: ot1lcmss.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions
))
\c@minutes=\count99
\c@seconds=\count100
\c@mv@invisible=\count101
LaTeX Font Info:    Overwriting symbol font `operators' in version `normal'
(Font)                  OT1/cmr/m/n --> OT1/lcmss/m/n on input line 424.
LaTeX Font Info:    Overwriting symbol font `letters' in version `normal'
(Font)                  OML/cmm/m/it --> OML/lcmm/m/it on input line 427.
LaTeX Font Info:    Overwriting symbol font `symbols' in version `normal'
(Font)                  OMS/cmsy/m/n --> OMS/lcmsy/m/n on input line 429.
LaTeX Font Info:    Overwriting symbol font `largesymbols' in version `normal'
(Font)                  OMX/cmex/m/n --> OMX/lcmex/m/n on input line 431.
LaTeX Font Info:    Overwriting symbol font `operators' in version `invisible'
(Font)                  OT1/cmr/m/n --> OT1/lcmss/m/In on input line 434.
LaTeX Font Info:    Overwriting symbol font `letters' in version `invisible'
(Font)                  OML/cmm/m/it --> OML/lcmm/m/Iit on input line 436.
LaTeX Font Info:    Overwriting symbol font `symbols' in version `invisible'
(Font)                  OMS/cmsy/m/n --> OMS/lcmsy/m/In on input line 438.
LaTeX Font Info:    Overwriting symbol font `largesymbols' in version `invisibl
e'
(Font)                  OMX/cmex/m/n --> OMX/lcmex/m/In on input line 440.
LaTeX Info: Redefining \rm on input line 526.
LaTeX Info: Redefining \sf on input line 527.
LaTeX Info: Redefining \tt on input line 528.
LaTeX Info: Redefining \bf on input line 529.
LaTeX Info: Redefining \it on input line 530.
LaTeX Info: Redefining \sl on input line 531.
LaTeX Info: Redefining \sc on input line 532.
LaTeX Info: Redefining \cal on input line 533.
LaTeX Info: Redefining \mit on input line 534.
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/graphicx.sty
Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)

(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/keyval.sty
Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
\KV@toks@=\toks20
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/graphics.sty
Package: graphics 2001/07/07 v1.0n Standard LaTeX Graphics (DPC,SPQR)

(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/graphics.cfg
File: graphics.cfg 2005/02/03 v1.3 graphics configuration of teTeX/TeXLive
)
Package graphics Info: Driver file: pdftex.def on input line 80.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/pdftex.def
File: pdftex.def 2002/06/19 v0.03k graphics/color for pdftex
\Gread@gobject=\count102
))
\Gin@req@height=\dimen112
\Gin@req@width=\dimen113
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/hyperref.sty
Package: hyperref 2003/11/30 v6.74m Hypertext links for LaTeX
\@linkdim=\dimen114
\Hy@linkcounter=\count103
\Hy@pagecounter=\count104

(/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/pd1enc.def
File: pd1enc.def 2003/11/30 v6.74m Hyperref: PDFDocEncoding definition (HO)
)
(/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/hyperref.cfg
File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive and teTeX
)
Package hyperref Info: Hyper figures OFF on input line 1880.
Package hyperref Info: Link nesting OFF on input line 1885.
Package hyperref Info: Hyper index ON on input line 1888.
Package hyperref Info: Plain pages ON on input line 1893.
Package hyperref Info: Backreferencing OFF on input line 1900.

Implicit mode ON; LaTeX internals redefined
Package hyperref Info: Bookmarks ON on input line 2004.
(/usr/local/teTeX/share/texmf.tetex/tex/latex/url/url.sty
\Urlmuskip=\muskip11
Package: url 2004/03/15  ver 3.1  Verb mode for urls, etc.
)
LaTeX Info: Redefining \url on input line 2143.
\Fld@menulength=\count105
\Field@Width=\dimen115
\Fld@charsize=\dimen116
\Choice@toks=\toks21
\Field@toks=\toks22
Package hyperref Info: Hyper figures OFF on input line 2618.
Package hyperref Info: Link nesting OFF on input line 2623.
Package hyperref Info: Hyper index ON on input line 2626.
Package hyperref Info: backreferencing OFF on input line 2633.
Package hyperref Info: Link coloring OFF on input line 2638.
\c@Item=\count106
\c@Hfootnote=\count107
)
*hyperref using default driver hpdftex*
(/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/hpdftex.def
File: hpdftex.def 2003/11/30 v6.74m Hyperref driver for pdfTeX

(/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/pifont.sty
Package: pifont 2004/09/15 PSNFSS-v9.2 Pi font support (SPQR) 
LaTeX Font Info:    Try loading font information for U+pzd on input line 63.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/upzd.fd
File: upzd.fd 2001/06/04 font definitions for U/pzd.
)
LaTeX Font Info:    Try loading font information for U+psy on input line 64.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/upsy.fd
File: upsy.fd 2001/06/04 font definitions for U/psy.
))
\Fld@listcount=\count108
\@outlinefile=\write3
)
Package hyperref Info: Option `colorlinks' set `true' on input line 19.

(./computation.aux)
\openout1 = `computation.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for OT1/lcmss/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.
LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 52.
LaTeX Font Info:    ... okay on input line 52.

(/usr/local/teTeX/share/texmf.tetex/tex/context/base/supp-pdf.tex
(/usr/local/teTeX/share/texmf.tetex/tex/context/base/supp-mis.tex
loading : Context Support Macros / Miscellaneous (2004.10.26)
\protectiondepth=\count109
\scratchcounter=\count110
\scratchtoks=\toks23
\scratchdimen=\dimen117
\scratchskip=\skip46
\scratchmuskip=\muskip12
\scratchbox=\box28
\scratchread=\read1
\scratchwrite=\write4
\zeropoint=\dimen118
\onepoint=\dimen119
\onebasepoint=\dimen120
\minusone=\count111
\thousandpoint=\dimen121
\onerealpoint=\dimen122
\emptytoks=\toks24
\nextbox=\box29
\nextdepth=\dimen123
\everyline=\toks25
\!!counta=\count112
\!!countb=\count113
\recursecounter=\count114
)
loading : Context Support Macros / PDF (2004.03.26)
\nofMPsegments=\count115
\nofMParguments=\count116
\MPscratchCnt=\count117
\MPscratchDim=\dimen124
\MPnumerator=\count118
\everyMPtoPDFconversion=\toks26
) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/color.sty
Package: color 1999/02/16 v1.0i Standard LaTeX Color (DPC)
LaTeX Info: Redefining \color on input line 71.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/color.cfg
File: color.cfg 2005/02/03 v1.3 color configuration of teTeX/TeXLive
)
Package color Info: Driver file: pdftex.def on input line 125.
)
Package hyperref Info: Link coloring ON on input line 52.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/nameref.sty
Package: nameref 2003/12/03 v2.21 Cross-referencing by name of section
\c@section@level=\count119
)
LaTeX Info: Redefining \ref on input line 52.
LaTeX Info: Redefining \pageref on input line 52.

(./computation.out) (./computation.out)
\openout3 = `computation.out'.

 [1


{/usr/local/teTeX/share/texmf.local/fonts/map/pdftex/updmap/pdftex.map}]
LaTeX Font Info:    Try loading font information for OML+lcmm on input line 81.


(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omllcmm.fd
File: omllcmm.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions
)
LaTeX Font Info:    Try loading font information for OMS+lcmsy on input line 81
.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omslcmsy.fd
File: omslcmsy.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions
)
LaTeX Font Info:    Try loading font information for OMX+lcmex on input line 81
.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omxlcmex.fd
File: omxlcmex.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions
)
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <34.4> on input line 81.
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <28.66> on input line 81.
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <23.89> on input line 81.
LaTeX Font Info:    Try loading font information for U+msa on input line 81.

(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/umsa.fd
File: umsa.fd 2002/01/19 v2.2g AMS font definitions
)

LaTeX Font Warning: Font shape `U/msa/m/n' in size <34.4> not available
(Font)              size <24.88> substituted on input line 81.


LaTeX Font Warning: Font shape `U/msa/m/n' in size <28.66> not available
(Font)              size <24.88> substituted on input line 81.


LaTeX Font Warning: Font shape `U/msa/m/n' in size <23.89> not available
(Font)              size <24.88> substituted on input line 81.

LaTeX Font Info:    Try loading font information for U+msb on input line 81.
(/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2002/01/19 v2.2g AMS font definitions
)

LaTeX Font Warning: Font shape `U/msb/m/n' in size <34.4> not available
(Font)              size <24.88> substituted on input line 81.


LaTeX Font Warning: Font shape `U/msb/m/n' in size <28.66> not available
(Font)              size <24.88> substituted on input line 81.


LaTeX Font Warning: Font shape `U/msb/m/n' in size <23.89> not available
(Font)              size <24.88> substituted on input line 81.

LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <19.907> on input line 85.
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <16.59> on input line 85.
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <13.82> on input line 85.

LaTeX Font Warning: Font shape `U/msa/m/n' in size <19.907> not available
(Font)              size <20.74> substituted on input line 85.


LaTeX Font Warning: Font shape `U/msa/m/n' in size <16.59> not available
(Font)              size <17.28> substituted on input line 85.


LaTeX Font Warning: Font shape `U/msa/m/n' in size <13.82> not available
(Font)              size <14.4> substituted on input line 85.


LaTeX Font Warning: Font shape `U/msb/m/n' in size <19.907> not available
(Font)              size <20.74> substituted on input line 85.


LaTeX Font Warning: Font shape `U/msb/m/n' in size <16.59> not available
(Font)              size <17.28> substituted on input line 85.


LaTeX Font Warning: Font shape `U/msb/m/n' in size <13.82> not available
(Font)              size <14.4> substituted on input line 85.

[2] [3] [4]
LaTeX Font Info:    Try loading font information for OMS+lcmss on input line 19
4.
LaTeX Font Info:    No file OMSlcmss.fd. on input line 194.


LaTeX Font Warning: Font shape `OMS/lcmss/m/n' undefined
(Font)              using `OMS/cmsy/m/n' instead
(Font)              for symbol `textbraceleft' on input line 194.


LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <19.907> not available
(Font)              size <20.74> substituted on input line 194.


LaTeX Font Warning: Font shape `OMS/lcmss/m/n' in size <19.907> not available
(Font)              size <20.74> substituted on input line 194.

[5] [6] [7] [8]

LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <19.907> not available
(Font)              size <20.74> substituted on input line 281.


LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <16.59> not available
(Font)              size <17.28> substituted on input line 281.


LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <13.82> not available
(Font)              size <14.4> substituted on input line 281.

[9] [10] [11] [12]

LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <34.4> not available
(Font)              size <24.88> substituted on input line 343.


LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <28.66> not available
(Font)              size <24.88> substituted on input line 343.


LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <23.89> not available
(Font)              size <24.88> substituted on input line 343.

[13] [14] [15] [16] [17] [18]
<DFA-even-odd.jpg, id=191, 325.215pt x 255.95625pt>
File: DFA-even-odd.jpg Graphic file (type jpg)
 <use DFA-even-odd.jpg>
[19 <./DFA-even-odd.jpg>] [20] [21]
<RNP-1-motif.jpg, id=206, 301.125pt x 95.3964pt>
File: RNP-1-motif.jpg Graphic file (type jpg)
 <use RNP-1-motif.jpg> [22 <./RNP-1-motif.jpg>] [23] [24] [25] [26] [27] [28]
<ACGT-Markov.jpg, id=238, 118.5228pt x 112.5003pt>
File: ACGT-Markov.jpg Graphic file (type jpg)
 <use ACGT-Markov.jpg>
<Pairwise-align-HMM.jpg, id=239, 314.3745pt x 233.9139pt>
File: Pairwise-align-HMM.jpg Graphic file (type jpg)

<use Pairwise-align-HMM.jpg> [29 <./ACGT-Markov.jpg> <./Pairwise-align-HMM.jpg>
] [30] [31] [32] [33] [34] [35]
<yeast-tRNA-Phe.jpg, id=271, 195.8517pt x 244.7544pt>
File: yeast-tRNA-Phe.jpg Graphic file (type jpg)
 <use yeast-tRNA-Phe.jpg>
Overfull \hbox (38.0pt too wide) in paragraph at lines 774--780
[]  
 []

[36 <./yeast-tRNA-Phe.jpg>] [37] [38] [39] [40] [41] [42] [43] [44] [45]
<Chomsky-hierarchy.jpg, id=318, 469.755pt x 343.2825pt>
File: Chomsky-hierarchy.jpg Graphic file (type jpg)

<use Chomsky-hierarchy.jpg>
Overfull \hbox (10.87393pt too wide) in paragraph at lines 934--948
[][]  
 []

[46 <./Chomsky-hierarchy.jpg>] [47] [48]
<Turing-Machine.jpg, id=332, 433.62pt x 289.08pt>
File: Turing-Machine.jpg Graphic file (type jpg)
 <use Turing-Machine.jpg>
[49 <./Turing-Machine.jpg>] [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59]
Overfull \hbox (38.0pt too wide) in paragraph at lines 1164--1167
[] 
 []


Overfull \hbox (38.0pt too wide) in paragraph at lines 1164--1167
[]  
 []

[60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72]
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <12> on input line 1337.
LaTeX Font Info:    External font `cmex10 at17.28pt' loaded for size
(Font)              <7> on input line 1337.
 [73] [74]
[75] [76] (./computation.aux)

LaTeX Font Warning: Size substitutions with differences
(Font)              up to 9.51999pt have occurred.


LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 ) 
Here is how much of TeX's memory you used:
 3851 strings out of 95217
 51397 string characters out of 1184538
 2096799 words of memory out of 4551634
 6749 multiletter control sequences out of 10000+50000
 18594 words of font info for 66 fonts, out of 2000000 for 2000
 58 hyphenation exceptions out of 1000
 27i,9n,24p,237b,372s stack positions out of 1500i,500n,5000p,200000b,5000s
 497 PDF objects out of 300000
 159 named destinations out of 131072
 52 words of extra memory for PDF output out of 65536
</usr/local/teTeX/share/texmf.tetex/fonts/type1/bluesky/cm/cmti12.pfb></usr/l
ocal/teTeX/share/texmf.tetex/fonts/type1/bluesky/symbols/msbm10.pfb></usr/local
/teTeX/share/texmf.tetex/fonts/type1/bluesky/cm/cmex10.pfb></usr/local/teTeX/sh
are/texmf.tetex/fonts/type1/bluesky/cm/cmmi8.pfb></usr/local/teTeX/share/texmf.
tetex/fonts/type1/bluesky/latex/lcmssi8.pfb></usr/local/teTeX/share/texmf.tetex
/fonts/type1/bluesky/cm/cmsy10.pfb></usr/local/teTeX/share/texmf.tetex/fonts/ty
pe1/bluesky/symbols/msam10.pfb></usr/local/teTeX/share/texmf.tetex/fonts/type1/
bluesky/cm/cmsy8.pfb></usr/local/teTeX/share/texmf.tetex/fonts/type1/bluesky/la
tex/lcmss8.pfb></usr/local/teTeX/share/texmf.tetex/fonts/type1/bluesky/latex/lc
mssb8.pfb>
Output written on computation.pdf (76 pages, 903255 bytes).
