etandem.txt

emboss的linux版本的源代码

                                  etandem 



Function

   Looks for tandem repeats in a nucleotide sequence

Description

   etandem looks for tandem repeats in a sequence. It is normally used
   after equicktandem has been run to identify potential repeat sizes. It
   calculates a consensus for the repeat region and gives a score for how
   many matches there are to the consensus - the number of mismatches.

   Input sequences are converted into ACGT or N (so ambiguity codes are
   ignored).
   The score is +1 for a match, -1 for a mismatch.
   The first copy of a repeat is ignored.
   The highest score is kept for each start position and repeat size.

   The lowest score to be reported is set by the threshold score. The
   threshold score can be set on the command-line using the -threshold
   qualifier, the default is 20. For perfect repeats, the score is the
   length of the repeat (except for the first copy). Reduce the threshold
   score a little if you wish to to allow mismatches. Each mismatch
   scores -1 instead of +1 so it scores 2 less than a perfect match of
   the same number of bases.

   Running with a wide range of repeat sizes is inefficient. That is why
   equicktandem was written - to give a rapid estimate of the major
   repeat sizes.

Usage

   Here is a sample session with etandem

   The input sequence is the human herpesvirus tandem repeat.


% etandem -noorigfile 
Looks for tandem repeats in a nucleotide sequence
Input nucleotide sequence: tembl:hhtetra
Minimum repeat size [10]: 6
Maximum repeat size [6]: 
Output report [hhtetra.tan]: 

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -minrepeat          integer    [10] Minimum repeat size (Integer, 2 or
                                  higher)
   -maxrepeat          integer    [Same as -minrepeat] Maximum repeat size
                                  (Integer, same as -minrepeat or higher)
  [-outfile]           report     [*.etandem] Output report file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -threshold          integer    [20] Threshold score (Any integer value)
   -mismatch           boolean    Allow N as a mismatch
   -uniform            boolean    Allow uniform consensus
   -origfile           outfile    [*.etandem] Sanger Centre program tandem
                                  output file (optional)

   Associated qualifiers:

   "-sequence" 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

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   "-origfile" associated qualifiers
   -odirectory         string     Output directory

   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

   The input for etandem is a nucleotide sequence USA.

  Input files for usage example

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

  Database entry: tembl:hhtetra

ID   HHTETRA    standard; DNA; VRL; 1272 BP.
XX
AC   L46634; L46689;
XX
SV   L46634.1
XX
DT   06-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 3)
XX
DE   Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
XX
KW   telomeric repeat.
XX
OS   Human herpesvirus 7
OC   Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae.
XX
RN   [1]
RP   1-1272
RX   MEDLINE; 96079055.
RA   Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
RA   Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
RT   "Identification of human telomeric repeat motifs at the genome termini of
RT   human herpesvirus 7: structural analysis and heterogeneity";
RL   J. Virol. 69(12):8041-8045(1995).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1272
FT                   /db_xref="taxon:10372"
FT                   /organism="Human herpesvirus 7"
FT                   /strain="JI"
FT                   /clone="ED132'1.2"
FT   repeat_region   207..928
FT                   /note="long and complex repeat region composed of various
FT                   direct repeats, including TAACCC (TRS), degenerate copies
FT                   of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
FT   misc_signal     938..998
FT                   /note="pac2 motif"
FT   misc_feature    1009
FT                   /note="right genome terminus (...ACA)"
XX
SQ   Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
     aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca        6
0
     ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       12
0
     tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       18
0
     ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       24
0
     actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       30
0
     taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       36
0
     taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       42
0
     tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       48
0
     cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       54
0
     taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       60
0
     gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       66
0
     ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       72
0
     cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       78
0
     cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       84
0
     accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       90
0
     accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       96
0
     cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      102
0
     gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      108
0
     agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      114
0
     aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      120
0
     agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      126
0
     gttttcaagc tt                                                          127
2
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default etandem writes a 'table' report file.

  Output files for usage example

  File: hhtetra.tan

########################################
# Program: etandem
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: etandem
#    -noorigfile
#    -sequence tembl:hhtetra
#    -minrepeat 6
# Report_format: table
# Report_file: hhtetra.tan
########################################

#=======================================
#
# Sequence: HHTETRA     from: 1   to: 1272
# HitCount: 5
#
# Threshold: 20
# Minrepeat: 6
# Maxrepeat: 6
# Mismatch: No
# Uniform: No
#
#=======================================

  Start     End   Score   Size  Count Identity Consensus
    793     936     120      6     24     93.8 acccta
    283     420      90      6     23     84.8 taaccc
    432     485      38      6      9     90.7 ccctaa
    494     529      26      6      6     94.4 ccctaa
    568     597      24      6      5    100.0 aaccct

#---------------------------------------
#---------------------------------------

Data files

   None

Notes

   Running with a wide range of repeat sizes is inefficient. That is why
   equicktandem was written - to give a rapid estimate of the major
   repeat sizes.

References

   None.

Warnings

   None.

Diagnostics

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                     Description
   einverted    Finds DNA inverted repeats
   equicktandem Finds tandem repeats
   palindrome   Looks for inverted repeats in a nucleotide sequence

   Running with a wide range of repeat sizes is inefficient. That is why
   equicktandem was written - to give a rapid estimate of the major
   repeat sizes.

Authors

   This program was originally written by Richard Durbin
   (rd