diffseq.txt

emboss的linux版本的源代码

                                  diffseq 



Function

   Find differences between nearly identical sequences

Description

   diffseq takes two overlapping, nearly identical sequences and reports
   the differences between them, together with any features that overlap
   with these regions. GFF files of the differences in each sequence are
   also produced.

   diffseq finds the region of overlap of the input sequences and then
   reports differences within this region, like a local alignment.

   The start and end positions of the overlap are reported.

   diffseq should be of value when looking for SNPs, differences between
   strains of an organism and anything else that requires the differences
   between sequences to be highlighted.

   The sequences can be very long. The program does a match of all
   sequence words of size 10 (by default). It then reduces this to the
   minimum set of overlapping matches by sorting the matches in order of
   size (largest size first) and then for each such match it removes any
   smaller matches that overlap. The result is a set of the longest
   ungapped alignments between the two sequences that do not overlap with
   each other. The mismatched regions between these matches are reported.

   It should be possible to find differences between sequences that are
   Mega-bases long.

Usage

   Here is a sample session with diffseq


% diffseq tembl:ap000504 tembl:af129756 
Find differences between nearly identical sequences
Word size [10]: 
Output report [ap000504.diffseq]: 
Features output [AP000504.diffgff]: 
Second features output [AF129756.diffgff]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
   -wordsize           integer    [10] The similar regions between the two
                                  sequences are found by creating a hash table
                                  of 'wordsize'd subsequences. 10 is a
                                  reasonable default. Making this value larger
                                  (20?) may speed up the program slightly,
                                  but will mean that any two differences
                                  within 'wordsize' of each other will be
                                  grouped as a single region of difference.
                                  This value may be made smaller (4?) to
                                  improve the resolution of nearby
                                  differences, but the program will go much
                                  slower. (Integer 2 or more)
  [-outfile]           report     [*.diffseq] Output report file name
  [-aoutfeat]          featout    [$(asequence.name).diffgff] File for output
                                  of first sequence's features
  [-boutfeat]          featout    [$(bsequence.name).diffgff] File for output
                                  of second sequence's features

   Additional (Optional) qualifiers:
   -globaldifferences  boolean    [N] Normally this program will find regions
                                  of identity that are the length of the
                                  specified word-size or greater and will then
                                  report the regions of difference between
                                  these matching regions. This works well and
                                  is what most people want if they are working
                                  with long overlapping nucleic acid
                                  sequences. You are usually not interested in
                                  the non-overlapping ends of these
                                  sequences. If you have protein sequences or
                                  short RNA sequences however, you will be
                                  interested in differences at the very ends .
                                  It this option is set to be true then the
                                  differences at the ends will also be
                                  reported.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -rformat3           string     Report format
   -rname3             string     Base file name
   -rextension3        string     File name extension
   -rdirectory3        string     Output directory
   -raccshow3          boolean    Show accession number in the report
   -rdesshow3          boolean    Show description in the report
   -rscoreshow3        boolean    Show the score in the report
   -rusashow3          boolean    Show the full USA in the report
   -rmaxall3           integer    Maximum total hits to report
   -rmaxseq3           integer    Maximum hits to report for one sequence

   "-aoutfeat" associated qualifiers
   -offormat4          string     Output feature format
   -ofopenfile4        string     Features file name
   -ofextension4       string     File name extension
   -ofdirectory4       string     Output directory
   -ofname4            string     Base file name
   -ofsingle4          boolean    Separate file for each entry

   "-boutfeat" associated qualifiers
   -offormat5          string     Output feature format
   -ofopenfile5        string     Features file name
   -ofextension5       string     File name extension
   -ofdirectory5       string     Output directory
   -ofname5            string     Base file name
   -ofsingle5          boolean    Separate file for each entry

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   This program reads in two nucleic acid sequence USAs or two protein
   sequence USAs.

  Input files for usage example

   'tembl:ap000504' is a sequence entry in the example nucleic acid
   database 'tembl'

  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