einverted.txt

emboss的linux版本的源代码

                                 einverted 



Function

   Finds DNA inverted repeats

Description

   einverted looks for inverted repeats (stem loops) in a nucleotide
   sequence.

   It will find inverted repeats that include a proprtion of mismatches
   and gaps (bulges in the stem loop).

Algorithm

   It works by finding alignments between the sequence and its reverse
   complement that exceed a threshold score. Gaps and Mismatches are
   assigned a penalty (negative) score. Matches are assigned a positive
   score. The score is calculated by summing the values of each match,
   the penalties of each mismatch and the large penalties of any gaps.
   Any region whose score exceeds the threshold is reported.

   einverted uses dynamic programming and thus is guaranteed to find the
   optimal alignment, but is slower than, for example, a self-by-self
   BLAST. It can find multiple inverted repeats in a sequence.

   einverted does not report overlapping matches.

   The original "inverted" program was written to annotate the nematode
   genome. Excluding overlapping repeats saved problems with simple
   repeat sequences in this genome.

Usage

   Here is a sample session with einverted


% einverted tembl:hsts1 
Finds DNA inverted repeats
Gap penalty [12]: 
Minimum score threshold [50]: 
Match score [3]: 
Mismatch score [-4]: 
Sanger Centre program inverted output file [hsts1.inv]: 
File for sequence of regions of inverted repeats. [hsts1.fasta]: 

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -gap                integer    [12] Gap penalty (Any integer value)
   -threshold          integer    [50] Minimum score threshold (Any integer
                                  value)
   -match              integer    [3] Match score (Any integer value)
   -mismatch           integer    [-4] Mismatch score (Any integer value)
  [-outfile]           outfile    [*.einverted] Sanger Centre program inverted
                                  output file
  [-outseq]            seqout     [.] The sequence of the
                                  inverted repeat regions without gap
                                  characters.

   Additional (Optional) qualifiers:
   -maxrepeat          integer    [2000] Maximum separation between the start
                                  of repeat and the end of the inverted repeat
                                  (the default is 2000 bases). (Any integer
                                  value)

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

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each 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
   -odirectory2        string     Output directory

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       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 einverted is a nucleotide sequence

  Input files for usage example

   'tembl:hsts1' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:hsts1

ID   HSTS1      standard; DNA; HUM; 18596 BP.
XX
AC   D00596;
XX
SV   D00596.1
XX
DT   17-JUL-1991 (Rel. 28, Created)
DT   27-OCT-1998 (Rel. 57, Last updated, Version 2)
XX
DE   Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7,
DE   complete cds.
XX
KW   thymidylate syntase.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-18596
RX   MEDLINE; 91056070.
RA   Kaneda S., Nalbantoglu J., Takeishi K., Shimizu K., Gotoh O., Seno T.,
RA   Ayusawa D.;
RT   "Structural and Functional Analysis of the Human Thymidylate Synthase
RT   Gene";
RL   J. Biol. Chem. 265:20277-20284(1990).
XX
DR   SWISS-PROT; P04818; TYSY_HUMAN.
XX
CC   These data kindly submitted in computer readable form by:
CC   Sumiko Kaneda
CC   National Institute of Genetics
CC   1111 Yata
CC   Mishima 411
CC   Japan
CC   Phone:  [phone]
CC   Fax:    [phone]
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..18596
FT                   /chromosome="18"
FT                   /db_xref="taxon:9606"
FT                   /sequenced_mol="DNA"
FT                   /organism="Homo sapiens"
FT                   /clone="lambdaHTS-1 and lambdaHTS-3"
FT                   /map="18p11.32"
FT   repeat_unit     1..148
FT                   /note="Alu sequence"
FT   repeat_unit     202..477


  [Part of this file has been deleted for brevity]

     ttttgttttt agcttcagcg agaacccaga cctttcccaa agctcaggat tcttcgaaaa     1566
0
     gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat     1572
0
     ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg     1578
0
     tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa     1584
0
     aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc     1590
0
     actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg     1596
0
     agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct     1602
0
     tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt     1608
0
     cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca     1614
0
     aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa     1620
0
     agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt     1626
0
     gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct     1632
0
     ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga     1638
0
     aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa     1644
0
     tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa     1650
0
     gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt     1656
0
     gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt     1662
0
     aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat     1668
0
     ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta     1674