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1 -=- run-mummer1 (MUMmer1.0) README -=-
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2
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3 ** NOTE **
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4 This manual is outdated, please refer to the HTML documentation included in
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5 this distribution or at:
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6
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7 http://mummer.sourceforge.net
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8 http://mummer.sourceforge.net/manual
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9 http://mummer.sourceforge.net/examples
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10
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11 This is the README for the original MUMmer 1.0 system, which is
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12 included in the MUMmer 3 package. It is slower and uses more memory,
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13 but it does have some slightly different functions and output so we
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14 make it available.
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15
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16
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17
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18 MUMmer 1.0 code and documentation are copyright (c) 1999 by The Institute
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19 for Genomic Research. The principle architect for the system was
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20 Arthur Delcher.
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21
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22 This directory contains the source code for MUMmer program for
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23 aligning long DNA sequences. If you use this code in any publication,
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24 please cite the following:
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25 A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson,
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26 O. White, and S.L. Salzberg. Alignment of whole genomes.
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27 Nucleic Acids Research, 27:11 (1999), 2369-2376.
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28
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29 MUMmer works on Unix only. This README file is the only documentation
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30 besides the code itself. Since it is free, we cannot provide any
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31 other support. The system is very easy to use, but you need to invest
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32 a few minutes up front reading this file and figuring out how to
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33 interpret the output. If you discover bugs, we would be interested in
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34 hearing about them so we can correct them. Address bug reports to
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35 <mummer-help@lists.sourceforge.net>. The system uses a LOT of RAM - if
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36 it crashes for that reason, that's not a bug. We recommend at least
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37 512Mb to align most pairs of bacterial genomes, and 1Gb or more may be
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38 required.
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39
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40 To use this system, first compile it by typing 'make' at the
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41 command line. There is a script, 'run-mummer1.csh', that runs all
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42 the steps of aligning two genomes. The script takes these arguments:
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43
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44 run-mummer1.csh <genome1> <genome2> <tag> [-r]
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45
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46 The two genomes must DNA sequences in FASTA format. Multi-FASTA
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47 files don't work. The tag is used to create 4 output files,
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48 all with 'tag' as a prefix. -flip will reverse complement <genome2>.
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49
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50 Of the four output files, two are intended for your inspection.
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51 <tag>.errorsgaps lists the alignment of all the MUMs (maximal unique
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52 matches - read the paper for definitions), and includes the longest
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53 ascending sequence of MUMs first. This sequence is the best alignment
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54 of the two genomes by the program. In between the MUMs are gaps,
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55 which are aligned using a Smith-Waterman implementation of our own.
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56 Those Smith-Waterman's are contained in the file <tag>.align.
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57 This can be a very long file if there are lots of gaps. If either
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58 of the two gaps is too long (over 5000bp), then the alignment is
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59 not performed.
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60
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61 IMPORTANT: the performance of the program can critically depend on the
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62 minimum MUM length you use. The default is 20bp. If you want to
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63 change it, do the following: edit the file run-mummer1.csh. Add a new
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64 length switch to the 'mummer' call.
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65
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66 The other file - one that we often spend lots of time analyzing - is
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67 <tag>.errorsgaps. The lines in that file are the MUMs, for example:
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68 46989 271588 23 none 3262 3304 1022
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69 47013 271612 24 none 1 1 1
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70 Columns 1 and 2 are the positions of a MUM in genomes 1 and 2. The
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71 MUM is 24bp in length, shown in column 3. Column 4 is the overlap
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72 from the previous MUM - usually this will be 'none' except when there
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73 are repeats present. Columns 5 and 6 show the gaps from the *end*
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74 of the previous MUM. Column 7 shows the number of errors - indels
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75 or mismatches - in the S-W alignment of the gap before this MUM.
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76 Hence in the two lines shown here, the second line is a MUM of 24bp,
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77 and it follows the previous MUM after a gap of just 1bp in each genome.
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78 This indicates a single nucleotide polymorphism.
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79
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80 Files in this directory:
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81
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82 annotate.cc Adds alignment info to gaps file produced by gaps
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83 or gaps2 . Reads frag info from the file named on the '>'
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84 lines of the gap file. The word "reverse" after that name
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85 will make that sequence get reverse-complemented.
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86 Also produces file witherrors.gaps which is the same as the
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87 gaps input file, put with an extra column of number of
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88 errors.
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89
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90 gaps.cc Finds longest consistent set of matches in list
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91 produced by mummer1 program.
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92
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93 run-mummer1.csh Script to run alignment programs. Format is:
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94 run-mummer1.csh <genome1> <genome2> <tag> [-flip]
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95 <tag> will be used to make output files: <tag>.out , <tag>.gaps
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96 and <tag>.align . -r will reverse complement <genome2>
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97
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98 Email questions, comments or bug reports to: <mummer-help@lists.sourceforge.net>
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99
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