dotpath.txt

emboss的linux版本的源代码

0
     atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt    18354
0
     gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca    18360
0
     agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc    18366
0
     cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca    18372
0
     atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct    18378
0
     tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt    18384
0
     ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc    18390
0
     tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc    18396
0
     tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg    18402
0
     gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg    18408
0
     cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa    18414
0
     aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg    18420
0
     atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata    18426
0
     tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat    18432
0
     gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg    18438
0
     ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca    18444
0
     tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag    18450
0
     gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac    18456
0
     ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc    18462
0
     tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc                   18466
6
//

  Database entry: tembl:AP000504

ID   AP000504   standard; DNA; HUM; 100000 BP.
XX
AC   AP000504; BA000025;
XX
SV   AP000504.1
XX
DT   28-SEP-1999 (Rel. 61, Created)
DT   22-AUG-2001 (Rel. 68, Last updated, Version 3)
XX
DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section
DE   3/20.
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-100000
RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
RT   ;
RL   Submitted (21-SEP-1999) to the EMBL/GenBank/DDBJ databases.
RL   Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced
RL   Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan
RL   (E-mail:[e-mail], URL:http://www-alis.tokyo.jst.go.jp/,
RL   Tel:[phone], Fax:[phone])
XX
RN   [2]
RA   Shiina S., Tamiya G., Oka A., Inoko H.;
RT   "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region";
RL   Unpublished.
XX
DR   SWISS-PROT; O00299; CLI1_HUMAN.
DR   SWISS-PROT; O43196; MSH5_HUMAN.
DR   SWISS-PROT; O95445; APOM_HUMAN.
DR   SWISS-PROT; O95865; DDH2_HUMAN.
DR   SWISS-PROT; O95867; NG24_HUMAN.
DR   SWISS-PROT; P13862; KC2B_HUMAN.
XX
CC   This sequence is conducted by Tokai University as a JST sequencing
CC   Team.
CC   Principal Investigator: Hidetoshi Inoko Ph.D
CC   Phone:[phone], Fax:[phone],
CC   The sequence is submitted by Human Genome Sequencing in ALIS
CC   project of JST
CC   Japan Science and Technology Corporation (JST)
CC   5-3, Yonbancyo, Chiyoda-ku, Tokyo, 102-0081 Japan
CC   For further infomation about this sequences, please visit our
CC   sequence archive Web site (http://www-alis.tokyo.jst.go.jp/HGS/top.


  [Part of this file has been deleted for brevity]

     gggtggatca tgaggtcaag agatcgagac tatcctggct aacatgatga aaccccgtct     9708
0
     ctactaaaaa tacaaaaaat tagctgggca tggtggcggg cacctgtagt cccagctact     9714
0
     cgggaggctg agtcaggaga atggtgtgaa cccaggagac ggagcttgca gtgagctgag     9720
0
     gtcgcaccac tgcactccag cctgggtgat agagcgagac tctgtctcaa aaaaaaaaaa     9726
0
     aaaaaaaaaa aaaacaaaaa ttagccgggt gtggtggcag gcaacttaat cccagctact     9732
0
     tgggaggcag aggcaggaga atcgtttgaa cctgggaggc ggaggttgaa gagaatagaa     9738
0
     gctctgctgg tccagagaag gattgggcca gggctctggg agaccaggga gaaagagggc     9744
0
     acatgtggtc cctgttgact gtgagggtgg gaatctgagg aaggctttgg ctcattgccc     9750
0
     cttgggtttg tccacagcca tccttcccct gcggagtatg tcgaggtgct ccaggagcta     9756
0
     cagcggctgg agagtcgcct ccagcccttc ttgcagcgct actacgaggt tctgggtgct     9762
0
     gctgccacca cggactacaa taacaatgtg agccctttga tggccctgcc ctttctcctc     9768
0
     agccccagta ctcccaaaac agaacaggct gaaatacaga taactctttc cctccctgga     9774
0
     aaaacattgc aacagggcca ggtgcagtgg ctcacgcctg taatcccagc actttgggag     9780
0
     gccaaggtgg gcggatcatc tgagatcggg agtttgagac cagcctggcc aacatggtgc     9786
0
     aaccccatct ctactgaaaa tataaacatt agctggatgt agtggtgcac acctgtaatc     9792
0
     ccagctactc aggaggctga ggcaggagaa tcgctagaac tcgggaggag ggggttgcag     9798
0
     tgagccgaga ttgcactact gcactctagc ctgggtgaca gagcgagact gtctcaaaaa     9804
0
     acaaaacaaa acaaaaaaac acacattgca acaaaacaat ttctctctaa acctgtaagt     9810
0
     gattttgtcc tcccttacag agaaggtgat aatctttgct gtaagcactg tcctcgtatc     9816
0
     gtaccccttg tgcccctgaa tgaatttaga aaatgtaaag tacaggagat cagtatatga     9822
0
     tgacttactg attcatagta gtgttttaat aggatgttcc ttatgtgaat aagatataat     9828
0
     ttatttgcaa agatttggtc tacatgtaaa cttccaagga tataactgaa agttttggag     9834
0
     gacatggtat tctcagtagg cattattgct tttattagtg agatggactc cagcttgata     9840
0
     ttttctgcct ttttgtgttt ggctggttgt gcgcagcacg agggccggga ggaggatcag     9846
0
     cggttgatca acttggtagg ggagagcctg cgactgctgg gcaacacctt tgttgcactg     9852
0
     tctgacctgc gctgcaatct ggcctgcacg cccccacgac acctgcatgt ggtccggcct     9858
0
     atgtctcact acaccacccc catggtgctc cagcaggcag ccattcccat acaggtgggt     9864
0
     tagggggagt ctggcctgag ggagagtgag gggtgttgat agagtgaccc agggtagcta     9870
0
     ctgggcctga aggaggttag gaaaggagga gactggaaac atggtgatga aggctggaga     9876
0
     tactttagag gtttatcatg aggttttctt ggttaggctc ttgtattttt ctcacatctg     9882
0
     cctgtccatc tgtctttttc agatcaatgt gggaaccact gtgaccatga caggaaatgg     9888
0
     gactcggccc cccccaactc ccaatgcaga ggcacctccc cctggtcctg ggcaggcctc     9894
0
     atccgtggct ccgtcttcta ccaatgtcga gtcctcagct gagggggctc ccccgccagg     9900
0
     tccagctccc ccgccagcca ccagccaccc gagggtcatc cggatttccc accagagtgt     9906
0
     ggaacccgtg gtcatgatgc acatgaacat tcaaggtgag aatagttgct ggcgagaaga     9912
0
     gcaggatcag catgatgagg gaggttcatg ctgaggtgtg agggaacagg gtggggaagg     9918
0
     gagaggcaca tgctggtggt ggtagcctgg ggaccagagc agaagcttaa gtagacagat     9924
0
     gtggggggtg tgggggttgg tttgtctttg gaggtgtgtt tgtgtggtga agggagtacc     9930
0
     tctccctgtt tagatggagg gaaaggcagg ctttctgatt gggggattat gggcctgaag     9936
0
     tatgcctgat ctcagaagga tatagttagg ccttggccct acctacctca gggccactgt     9942
0
     ctctgtctcc ctgcccagat tctggcacac agcctggtgg tgttccgagt gctcccactg     9948
0
     gccccctggg accccctggt catggccaaa ccctgggtaa gagtgagggc atcagggcag     9954
0
     gctgagctct gggtagagaa agggaagggc tgagtgggtg ggttgaaggg gtccaggttc     9960
0
     aaggttacat cagacccgcc ccccaggctc caccctcatc cagctgccct ccctgccccc     9966
0
     tgagttcatg cacgccgtcg cccaccagat cactcatcag gccatggtgg cagctgttgc     9972
0
     ctccgcggcc gcaggtaatg acctggaagg ggaggcttgg gaggtagggc acagtccatg     9978
0
     gtggcagctg gctggcaagg gcctggccct cagccctctt cggtctgtct cttctgccac     9984
0
     ccacaggaca gcaggtgcca ggcttcccaa cagctccaac ccgggtggtg attgcccggc     9990
0
     ccactcctcc acaggctcgg ccttcccatc ctggagggcc cccagtctct gggacactgg     9996
0
     tgagcaaggg tcggggagtt ctagtgcgta acagtctagg                          10000
0
//

Output file format

   In normal operation, a dotplot image is displayed.

   With the -data qualifier a file of the positions of the matches in the
   minimal non-overlapping set of matches is output.

  Output files for usage example

  Graphics File: dotpath.ps

   [dotpath results]

Notes

   None

References

   None

Warnings

   If you give a small word size with a very large sequence you will run
   out of memory. If this happens, try again with a larger word size.

Diagnostic Error Messages

   None

Exit status

   It always exits with status 0.

Known bugs

   None

See also

   Program name                       Description
   dotmatcher   Displays a thresholded dotplot of two sequences
   dottup       Displays a wordmatch dotplot of two sequences
   polydot      Displays all-against-all dotplots of a set of sequences

   This program is closely based on dottup with the addition of by
   default displaying only the minimal set of non-overlapping matches.

   This program uses the same algorithm as diffseq for finding a minimal
   set of very good matches between two sequences. diffseq may be more
   convenient if you are looking at the differences between two nearly
   identical sequences.

Author(s)

   Gary Williams (gwilliam