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BT
88.08 725.04  TD
0 0 0 rg 
/F0 11.68  Tf
0.0695  Tc -0.2295  Tw (The FASTA F) Tj
70.8 0  TD 0.095  Tc 0  Tw (ormat) Tj
30.48 0  TD 0.1004  Tc -0.1404  Tw ( [1]) Tj
16.56 0  TD 0  Tc -0.04  Tw ( ) Tj
-117.84 -12.24  TD /F1 10.7456  Tf
-0.0464  Tw ( ) Tj
0 -12.48  TD 0.0302  Tc -0.3166  Tw (The ) Tj
20.16 0  TD -0.0254  Tc 0.219  Tw (FASTA format ) Tj
68.88 0  TD -0.0237  Tc 0.5681  Tw (is a very simply format to describe nucleic acid or amino acid sequences. ) Tj
323.52 0  TD -0.0783  Tc 0  Tw (A) Tj
7.92 0  TD 0  Tc -0.0464  Tw ( ) Tj
-420.48 -12.48  TD -0.0128  Tc 0.2064  Tw (FASTA file ) Tj
54.48 0  TD -0.0332  Tc 0.4668  Tw (begins with a single) Tj
86.88 0  TD 0.0217  Tc 0  Tw (-) Tj
3.6 0  TD 0.0504  Tc 0.1432  Tw (line ) Tj
19.2 0  TD 0.0019  Tc 0.1917  Tw (containing a ) Tj
56.4 0  TD -0.0212  Tc 0  Tw (description) Tj
47.52 0  TD 0.0166  Tc 0.417  Tw ( of the sequence) Tj
70.8 0  TD 0.0193  Tc 0.3543  Tw (, followed by lines ) Tj
-338.88 -12.24  TD -0.0028  Tc -0.0436  Tw (of sequence data. ) Tj
76.56 0  TD 0  Tc -0.0464  Tw ( ) Tj
-76.56 -12.24  TD -0.0194  Tc 2.913  Tw (The description line is ) Tj
3.0127  Tc 0  Tw (i) Tj
112.56 0  TD 0.0667  Tc 2.7669  Tw (dentified by) Tj
54.48 0  TD -0.0051  Tc 2.8387  Tw ( a greater) Tj
45.84 0  TD 0.0217  Tc 0  Tw (-) Tj
3.36 0  TD -0.0181  Tc 3.0917  Tw (than \(">) Tj
38.4 0  TD -0.031  Tc 2.9606  Tw ("\) symbol in the first column.) Tj
0  Tc -0.0464  Tw ( ) Tj
146.4 0  TD -0.1628  Tc 0  Tw (It) Tj
6.48 0  TD 0.0163  Tc 3.0573  Tw ( is) Tj
0  Tc 0.1936  Tw ( ) Tj
-407.52 -12.24  TD 0.0033  Tc 0.7903  Tw (recommended that all lines of text ) Tj
154.56 0  TD -0.0164  Tc -0.03  Tw (should ) Tj
32.16 0  TD 0.0385  Tc 0.7151  Tw (be shorter than 80 characters in length) Tj
169.68 0  TD 0.0146  Tc 0.659  Tw (. For example, ) Tj
-356.4 -12.48  TD 0.0154  Tc 0.5142  Tw (from the description line it is clear that the FASTA file) Tj
242.16 0  TD 0.0132  Tc 0.6604  Tw ( AE00517) Tj
44.64 0  TD -0.1728  Tc 0  Tw (4v2) Tj
16.08 0  TD 0.0217  Tc (-) Tj
3.36 0  TD 0.0184  Tc 0.4152  Tw (1.fas file contains) Tj
77.04 0  TD -0.057  Tc 0.7306  Tw ( the) Tj
16.32 0  TD -0.0062  Tc 0.5598  Tw ( first ) Tj
-399.6 -12.24  TD 0.0074  Tc -0.1738  Tw (contig of the E.coli sequence:) Tj
126.96 0  TD 0  Tc -0.0464  Tw ( ) Tj
2.4 0  TD ( ) Tj
-129.36 -11.04  TD /F2 9.8112  Tf
0.1133  Tw ( ) Tj
0 -9.12  TD /F2 7.7088  Tf
0.0681  Tc 0  Tw (>AE005174) Tj
42 0  TD -0.0653  Tc (-) Tj
4.8 0  TD 0.0356  Tc 0.51  Tw (1 Genome sequence of enterohemorrhagic Escherichia coli O157:H7, segment 1 of 2.) Tj
378.24 0  TD 0  Tc -0.0653  Tw ( ) Tj
-425.04 -8.88  TD 0.0487  Tc 0  Tw (agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtctctgacagcagcttctgaactg) Tj
373.68 0  TD 0  Tc -0.0653  Tw ( ) Tj
-373.68 -8.88  TD 0.0438  Tc 0  Tw (gttacctgccgtgagtaaattaaaattttattgacttaggtcac) Tj
205.68 0  TD 0.0481  Tc (taaatactttaaccaatataggcatagcgcacagac) Tj
168 0  TD 0  Tc -0.0653  Tw ( ) Tj
-373.68 -8.88  TD 0.0487  Tc 0  Tw (agataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccaccaccatcacc) Tj
373.68 0  TD 0  Tc -0.0653  Tw ( ) Tj
-373.68 -8.64  TD 0.0487  Tc 0  Tw (attaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggct) Tj
373.68 0  TD 0  Tc -0.0653  Tw ( ) Tj
-338.64 -12  TD /F1 10.7456  Tf
-0.0464  Tw ( ) Tj
-35.04 -12.24  TD 0.0076  Tc 1.296  Tw (Sequences are expected to be represented in the standard) Tj
255.36 0  TD -0.003  Tc 1.3486  Tw ( IUB/IUPAC amino acid and nucleic) Tj
0  Tc -0.0464  Tw ( ) Tj
-255.36 -12.48  TD -0.0085  Tc 1.5941  Tw (acid codes, with these exceptions: lower) Tj
180.24 0  TD 0.0217  Tc 0  Tw (-) Tj
3.6 0  TD -0.0081  Tc 1.6117  Tw (case letters are accepted and are mapped into upper) Tj
233.04 0  TD 0.0217  Tc 0  Tw (-) Tj
-416.88 -12.24  TD 0.0217  Tc -0.1691  Tw (case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino ) Tj
0 -12.24  TD -0.0209  Tc 0.0545  Tw (acid sequences, U and * are ac) Tj
130.8 0  TD 0.0245  Tc -0.3109  Tw (ceptable ) Tj
38.64 0  TD -0.0455  Tc -0.2409  Tw (query ) Tj
27.12 0  TD -0.0272  Tc -0.0992  Tw (letters \(see below\). ) Tj
83.52 0  TD 0  Tc -0.0464  Tw ( ) Tj
-280.08 -12.48  TD -0.016  Tc 1.0896  Tw (Before submitting a request) Tj
122.16 0  TD -0.0158  Tc 0  Tw (/query) Tj
27.12 0  TD 0.0111  Tc 0.9985  Tw (, any numerical digits in the query sequence should either be) Tj
0  Tc -0.2864  Tw ( ) Tj
-149.28 -12  TD -0.0121  Tc 0.8507  Tw (removed or replaced by appropriate letter codes \(e.g., N for unknown nucleic acid residue or X ) Tj
0 -12.48  TD -0.0077  Tc -0.1587  Tw (for unknown amino acid residu) Tj
133.68 0  TD 0.0814  Tc 0  Tw (e\).) Tj
11.04 0  TD 0.0037  Tc -0.1221  Tw ( \(In the given E.coli FASTA sequence there are no numbers.\)) Tj
262.8 0  TD 0  Tc -0.0464  Tw ( ) Tj
-407.52 -12.48  TD ( ) Tj
0 -12  TD -0.0088  Tc -0.0376  Tw (The nucleic acid codes supported are: ) Tj
163.92 0  TD 0  Tc -0.0464  Tw ( ) Tj
-163.92 -11.28  TD /F2 9.8112  Tf
-0.1267  Tc 0.08  Tw (        A ) Tj
58.32 0  TD 0.1133  Tc 0  Tw (--) Tj
11.76 0  TD -0.0394  Tc 0.005  Tw (> adenosine           M ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0307  Tc -0.016  Tw (> A C \(amino\)) Tj
75.84 0  TD 0  Tc 0.1133  Tw ( ) Tj
-297.84 -11.04  TD -0.1267  Tc 0.08  Tw (        C ) Tj
58.32 0  TD 0.1133  Tc 0  Tw (--) Tj
11.76 0  TD -0.0547  Tc 0.0309  Tw (> cytidine            S ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0613  Tc 0.0145  Tw (> G C \(strong\)) Tj
81.6 0  TD 0  Tc 0.1133  Tw ( ) Tj
-303.6 -11.04  TD -0.1267  Tc 0.08  Tw (        G ) Tj
58.32 0  TD 0.1133  Tc 0  Tw (--) Tj
11.76 0  TD -0.0467  Tc 0.016  Tw (> guanine             W ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0239  Tc -0.0229  Tw (> A T \(wea) Tj
58.32 0  TD -0.1267  Tc 0  Tw (k\)) Tj
11.76 0  TD 0  Tc 0.1133  Tw ( ) Tj
-292.08 -11.04  TD -0.0667  Tw (        ) Tj
46.8 0  TD -0.1267  Tc 0  Tw (T ) Tj
11.52 0  TD 0.1133  Tc (--) Tj
11.76 0  TD -0.0394  Tc 0.005  Tw (> thymidine           B ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0067  Tc -0.04  Tw (> G T C) Tj
40.8 0  TD 0  Tc 0.1133  Tw ( ) Tj
-262.8 -11.04  TD -0.0667  Tw (        ) Tj
46.8 0  TD -0.1267  Tc 0  Tw (U ) Tj
11.52 0  TD 0.1133  Tc (--) Tj
11.76 0  TD -0.0467  Tc 0.016  Tw (> uridine             D ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0067  Tc -0.04  Tw (> G A T) Tj
40.8 0  TD 0  Tc 0.1133  Tw ( ) Tj
-262.8 -11.04  TD -0.0667  Tw (        ) Tj
46.8 0  TD -0.1267  Tc 0  Tw (R ) Tj
11.52 0  TD 0.1133  Tc (--) Tj
11.76 0  TD -0.0267  Tc -0.02  Tw (> G A \(purine\)        H ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0067  Tc -0.04  Tw (> A C T) Tj
40.8 0  TD 0  Tc 0.1133  Tw ( ) Tj
-262.8 -10.8  TD -0.0667  Tw (        ) Tj
46.8 0  TD -0.1267  Tc 0  Tw (Y ) Tj
11.52 0  TD 0.1133  Tc (--) Tj
11.76 0  TD -0.0367  Tc (> T C \(pyrimidine\)    V ) Tj
140.16 0  TD -0.1267  Tc (--) Tj
11.76 0  TD -0.0067  Tc -0.04  Tw (> G C A) Tj
40.8 0  TD 0  Tc 0.1133  Tw ( ) Tj
-262.8 -11.28  TD -0.1267  Tc 0.08  Tw (        K ) Tj
58.32 0  TD 0.1133  Tc 0  Tw (--) Tj
11.76 0  TD -0.0307  Tc -0.0103  Tw (> G T \(keto\)          N ) Tj
140.16 0  TD -0.1267  Tc 0  Tw (--) Tj
11.76 0  TD -0.0547  Tc -0.024  Tw (> A G C T \(any\)) Tj
87.6 0  TD 0  Tc 0.1133  Tw ( ) Tj
-309.6 -11.04  TD -0.0307  Tw (               ) Tj
87.6 0  TD -0.0509  Tw (                   ) Tj
110.88 0  TD 0.1133  Tc 0  Tw (-) Tj
6 0  TD -0.0567  Tc 0.026  Tw (  gap of indeterminate length) Tj
169.2 0  TD 0  Tc 0.1133  Tw ( ) Tj
-373.68 -12  TD /F1 10.7456  Tf
-0.0147  Tc -0.0502  Tw (In our two FASTA files all these codes appear except for the code \221) Tj
289.2 0  TD 0.0217  Tc 0  Tw (-) Tj
3.6 0  TD -0.2523  Tc (\221.) Tj
6 0  TD 0  Tc -0.0464  Tw ( ) Tj
-298.8 -12.48  TD ( ) Tj
0 -12.24  TD 0.013  Tc 0.1806  Tw (Note that for ) Tj
58.56 0  TD 0.0327  Tc 0.3209  Tw (amino acid query sequ) Tj
98.16 0  TD -0.0113  Tc 0.4449  Tw (ences \(BLASTP and TBLASTN\)) Tj
144 0  TD -0.0484  Tc 0.242  Tw ( other) Tj
24.96 0  TD 0.0121  Tc 0.3615  Tw ( amino acid codes are) Tj
94.8 0  TD 0  Tc -0.0464  Tw ( ) Tj
-420.48 -12.24  TD -0.0086  Tc -0.2778  Tw (used \(see [1]\).) Tj
60.72 0  TD 0  Tc -0.0464  Tw ( ) Tj
2.64 0  TD ( ) Tj
-63.36 -12.48  TD ( ) Tj
0 -12.24  TD /F0 10.7456  Tf
-0.0268  Tc -0.0196  Tw (The Gene Positions) Tj
88.08 0  TD 0  Tc -0.0464  Tw ( ) Tj
-88.08 -12.24  TD /F1 10.7456  Tf
-0.0396  Tc 0.2332  Tw (The gene) Tj
39.6 0  TD -0.016  Tc 0.1136  Tw ( positions given in the zip) Tj
111.6 0  TD 0.0217  Tc 0  Tw (-) Tj
3.36 0  TD 0.0196  Tc -0.066  Tw (file \() Tj
20.64 0  TD 0.0306  Tc 0.163  Tw (and MS Exce) Tj
58.32 0  TD 0.0129  Tc 0.074  Tw (l file\) are given by the starting position and ) Tj
-233.52 -12.48  TD -0.0164  Tc 2.5227  Tw (ending position \(lend, en rend\) of the genes. These indicate the nucleotid) Tj
339.6 0  TD 0.0136  Tc 2.5  Tw (e positions in the) Tj
0  Tc 0.1936  Tw ( ) Tj
-339.6 -12.24  TD -0.0394  Tc -0.127  Tw (FASTA files \() Tj
60.96 0  TD -0.0146  Tc -0.0318  Tw (of course without counting new line characters etc.\). Furt) Tj
245.04 0  TD 0  Tc 0.0129  Tw (hermore, counting starts at ) Tj
-306 -12.24  TD 0.0268  Tc -0.0732  Tw (position 1.) Tj
45.36 0  TD 0  Tc -0.0464  Tw ( ) Tj
-45.36 -12.24  TD -0  Tc 0.3807  Tw (Therefore, to derive the location and sequence of the genes) Tj
257.28 0  TD -0.0464  Tc 0  Tw (,) Tj
2.64 0  TD 0  Tc 0.4335  Tw ( you have to write some simple code ) Tj
-259.92 -12.48  TD 0.0583  Tc -0.1047  Tw ([2, 3] ) Tj
26.88 0  TD 0.0148  Tc 0.3255  Tw (to read all the codes given in the FASTA file into a character array and do the appropriate ) Tj
-26.88 -12.24  TD 0.0027  Tc 0  Tw (counting.) Tj
39.84 0  TD 0  Tc -0.0464  Tw ( ) Tj
3.84 0  TD 0.0079  Tc 1.0257  Tw (This also ) Tj
1.1072  Tc 0  Tw (g) Tj
49.44 0  TD 0.0023  Tc 0.9852  Tw (ives an easy way to print statistics, tables, and special formatted files that ) Tj
-93.12 -12.24  TD -0.0043  Tc -0.0764  Tw (can be handled by the Hidden Markov Toolkits.) Tj
205.2 0  TD 0  Tc -0.1155  Tw ( \(See also the given GHMM DNA example.\)) Tj
192 0  TD 0  Tc -0.0464  Tw ( ) Tj
-397.2 -12.48  TD ( ) Tj
0 -12.48  TD /F0 10.7456  Tf
-0.0375  Tc 0  Tw (Reference) Tj
46.08 0  TD -0.1  Tc (s) Tj
4.08 0  TD 0  Tc -0.0464  Tw ( ) Tj
-50.16 -12  TD /F1 10.7456  Tf
0.0635  Tc -0.1099  Tw ([1] ) Tj
15.12 0  TD 0 0 1 rg 
-0.0486  Tc 0  Tw (http://www.ncb) Tj
66.96 0  TD -0.0217  Tc (i.nlm.nih.gov/blast/fasta.shtml) Tj
ET
103.2 138 197.04 0.48 re f
BT
300.24 139.68  TD
0 0 0 rg 
0  Tc -0.0464  Tw ( ) Tj
-212.16 -12.48  TD 0.0635  Tc -0.1099  Tw ([2] ) Tj
15.12 0  TD 0 0 1 rg 
-0.0213  Tc 0  Tw (http://bioweb.pasteur.fr/docs/seqio/seqio.html) Tj
ET
103.2 125.76 196.32 0.48 re f
BT
299.52 127.2  TD
0 0 0 rg 
0  Tc -0.0464  Tw ( ) Tj
-211.44 -12.24  TD 0.0635  Tc -0.1099  Tw ([3] ) Tj
15.12 0  TD 0.0286  Tc -0.155  Tw (Sample code for FASTA) Tj
107.04 0  TD 0.0217  Tc 0  Tw (-) Tj
3.6 0  TD -0.0427  Tc -0.0037  Tw (I/O and statistics: ) Tj
77.04 0  TD 0 0 1 rg 
-0.0099  Tc 0  Tw (http://www.liacs.nl/~erwin/dbdm2008/fasta_io.zip) Tj
ET
290.88 113.28 217.2 0.48 re f
BT
508.08 114.96  TD
0 0 0 rg 
0  Tc -0.0464  Tw ( ) Tj
ET
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