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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: edialign
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
edialign
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Local multiple alignment of sequences
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<b>edialign</b> is an EMBOSS version of the program DIALIGN2 by B.
Morgenstern. It takes as input nucleic acid or protein sequences and
produces as output a multiple sequence alignment. The sequences need
not be similar over their complete length, since the program
constructs alignments from gapfree pairs of similar segments of the
sequences. Such segment pairs are referred to as "diagonals". If
(possibly) coding nucleic acid sequences are to be aligned, <b>edialign</b>
can optionally translate the compared "nucleic acid segments" to
"peptide segments", or even perform comparisons at both nucleic acid
and protein levels, so as to increase the sensitivity of the
comparison.



<H2>
    Algorithm
</H2>

For a complete explanation of the algorithm, see the references. In short :

<p>
As described in our papers, the program DIALIGN constructs alignments
from gapfree pairs of similar segments of the sequences. Such segment
pairs are referred to as "diagonals".  Every possible diagonal is
given a so-called weight reflecting the degree of similarity among the
two segments involved. The overall score of an alignment is then
defined as the sum of weights of the diagonals it consists of and the
program tries to find an alignment with maximum score -- in other
words : the program tries to find a consistent collection of diagonals
with maximum sum of weights. This novel scoring scheme for alignments
is the basic difference between DIALIGN and other global or local
alignment methods. Note that DIALIGN does not employ any kind of gap
penalty.

<p>
It is possible to use a threshold T for the quality of the
diagonals. In this case, a diagonal is considered for alignment only
if its "weight" exceeds this threshold. Regions of lower similarity
are ignored.  In the first version of the program (DIALIGN 1), this
threshold was in many situations absolutely necessary to obtain
meaningful alignments. By contrast, DIALIGN 2 should produce
reasonable alignments without a threshold, i.e. with T = 0. This is
the most important difference between DIALIGN 2 and the first version
of the program. Nevertheless, it is still possible to use a positive
threshold T to filter out regions of lower significance and to include
only high scoring diagonals into the alignment.

<p>
The use of overlap weights improves the sensitivity of the program if
multiple sequences are aligned but it also increases the running time,
especially if large numbers of sequences are aligned. By default,
"overlap weights" are used if up to 35 sequences are aligned but
switched off for larger data sets.

<p>
If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN
optionally translates the compared "nucleic acid segments" to "peptide
segments" according to the genetic code -- without presupposing any of
the three possible reading frames, so all combinations of reading
frames get checked for significant similarity. If this option is used,
the similarity among segments will be assessed on the "peptide level"
rather than on the "nucleic acid level".

<p>
For the levels of sequence similarity, release 2.2 of DIALIGN has two
additional options:

<ul>
<li>
It can  measure the similarity among  segment pairs at  both levels of
similarity (nucleotide-level and  peptide-level similarity). The score
of  a fragment  is  based on  whatever  similarity is  stronger. As  a
result, the program can now produce mixed alignments that contain both
types  of  fragments.  Fragments   with  stronger  similarity  at  the
"nucleotide level"  are referred  to as N-fragments  whereas fragments
with stronger similarity a the peptide level are called P-fragments.

<li>
If the translation or mixed alignment option is used, it is possible
to consider the reverse complements of segments, too. In this case,
both the original segments and their reverse complements are
translated and both pairs of implied "peptide segments" are
compared. This option is useful if DNA sequences contain coding
regions not only on the "Watson strand" but also on the "Crick
strand".

</ul>

The score that DIALIGN assigns to a fragment is based on the
probability to find a fragment of the same respective length and
number of matches (or BLOSUM values, if the translation option is
used) in random sequences of the same length as the input
sequences. If long genomic sequences are aligned, an iterative
procedure can be applied where the program first looks for fragments
with strong similarity. In subsequent steps, regions between these
fragments are realigned. Here, the score of a fragment is based on
random occurrence in these regions between the previously aligned
segment pairs.


<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>edialign</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>edialign </b>
Local multiple alignment of sequences
Input sequence set: <b>vtest.seq</b>
Output file [vtest.edialign]: <b></b>
(gapped) output sequence(s) [vtest.fasta]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Local multiple alignment of sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     Sequence set filename and optional format,
                                  or reference (input USA)
  [-outfile]           outfile    [*.edialign] Output file name
  [-outseq]            seqoutall  [<sequence>.<format>] (Aligned) sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers (* if not always prompted):
*  -nucmode            menu       [n] Nucleic acid sequence alignment mode
                                  (simple, translated or mixed) (Values: n
                                  (simple); nt (translation); ma (mixed
                                  alignments))
*  -revcomp            boolean    [N] Also consider the reverse complement
   -overlapw           selection  [default (when Nseq =< 35)] By default
                                  overlap weights are used when Nseq =<35 but
                                  you can set this to 'yes' or 'no'
   -linkage            menu       [UPGMA] Clustering method to construct
                                  sequence tree (UPGMA, minimum linkage or
                                  maximum linkage) (Values: UPGMA (UPGMA); max
                                  (maximum linkage); min (minimum linkage))
   -maxfragl           integer    [40] Maximum fragment length (Integer 0 or
                                  more)
*  -fragmat            boolean    [N] Consider only N-fragment pairs that
                                  start with two matches
*  -fragsim            integer    [4] Consider only P-fragment pairs if first
                                  amino acid or codon pair has similarity
                                  score of at least n (Integer 0 or more)
   -itscore            boolean    [N] Use iterative score
   -threshold          float      [0.0] Threshold for considering diagonal for
                                  alignment (Number 0.000 or more)

   Advanced (Unprompted) qualifiers:
   -mask               boolean    [N] Replace unaligned characters by stars
                                  '*' rather then putting them in lowercase
   -dostars            boolean    [N] Activate writing of stars instead of
                                  numbers
   -starnum            integer    [4] Put up to n stars '*' instead of digits
                                  0-9 to indicate level of conservation
                                  (Integer 0 or more)

   Associated qualifiers:

   "-sequences" 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequences]<br>(Parameter 1)</td>
<td>seqset</td>
<td>Sequence set filename and optional format, or reference (input USA)</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.edialign</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outseq]<br>(Parameter 3)</td>
<td>seqoutall</td>
<td>(Aligned) sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-nucmode</td>
<td>list</td>
<td>Nucleic acid sequence alignment mode (simple, translated or mixed)</td>
<td><table><tr><td>n</td> <td><i>(simple)</i></td></tr><tr><td>nt</td> <td><i>(translation)</i></td></tr><tr><td>ma</td> <td><i>(mixed alignments)</i></td></tr></table></td>
<td>n</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-revcomp</td>
<td>boolean</td>
<td>Also consider the reverse complement</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-overlapw</td>
<td>selection</td>
<td>By default overlap weights are used when Nseq =&lt;35 but you can set this to 'yes' or 'no'</td>
<td>Choose from selection list of values</td>
<td>default (when Nseq =< 35)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-linkage</td>
<td>list</td>
<td>Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage)</td>
<td><table><tr><td>UPGMA</td> <td><i>(UPGMA)</i></td></tr><tr><td>max</td> <td><i>(maximum linkage)</i></td></tr><tr><td>min</td> <td><i>(minimum linkage)</i></td></tr></table></td>
<td>UPGMA</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-maxfragl</td>
<td>integer</td>
<td>Maximum fragment length</td>
<td>Integer 0 or more</td>
<td>40</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-fragmat</td>
<td>boolean</td>
<td>Consider only N-fragment pairs that start with two matches</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-fragsim</td>
<td>integer</td>
<td>Consider only P-fragment pairs if first amino acid or codon pair has similarity score of at least n</td>
<td>Integer 0 or more</td>
<td>4</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-itscore</td>
<td>boolean</td>
<td>Use iterative score</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-threshold</td>
<td>float</td>
<td>Threshold for considering diagonal for alignment</td>
<td>Number 0.000 or more</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-mask</td>
<td>boolean</td>
<td>Replace unaligned characters by stars '*' rather then putting them in lowercase</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-dostars</td>
<td>boolean</td>
<td>Activate writing of stars instead of numbers</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-starnum</td>
<td>integer</td>
<td>Put up to n stars '*' instead of digits 0-9 to indicate level of conservation</td>
<td>Integer 0 or more</td>
<td>4</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequences" associated seqset qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequences</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequences</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequences</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequences</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequences</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequences</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequences</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequences</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequences</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequences</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequences</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequences</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequences</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequences</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequences</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequences</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequences</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequences</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outseq" associated seqoutall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osformat3<br>-osformat_outseq</td>
<td>string</td>
<td>Output seq format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osextension3<br>-osextension_outseq</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osname3<br>-osname_outseq</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdirectory3<br>-osdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -osdbname3<br>-osdbname_outseq</td>
<td>string</td>
<td>Database name to add</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ossingle3<br>-ossingle_outseq</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oufo3<br>-oufo_outseq</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -offormat3<br>-offormat_outseq</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofname3<br>-ofname_outseq</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofdirectory3<br>-ofdirectory_outseq</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<b>edialign</b> reads nucleotide or protein sequences to be aligned.

<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.
<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: vtest.seq</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
&gt;HTL2  
LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAKPWP
SLNIFLDSKY
&gt;MMLV   
GKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIH
CPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL
&gt;HEPB 
RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNS
GRTSLYADSPSVPSHLPDRVH
</pre>
</td></tr></table><p>





<H2>
    Output file format
</H2>


<b>edialign</b> produces two output files with a multiple sequence
alignment. The first one is a file in DIALIGN format and the second
one is a sequence file in any format you choose (by default
fastA).

<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.
<p>
Capital letters denote aligned residues, i.e. residues
involved in at least one of the "diagonals" in the
alignment. Lower-case letters denote residues not belonging to any of
these selected "diagonals". They are not considered to be aligned by
DIALIGN. Thus, if a lower-case letter is standing in the same column
with other letters, this is pure chance ; these residues are not
considered to be homologous.

<p>
Numbers below the alignment reflect the degree of local similarity
among sequences. More precisely, they represent the sum of weights of
fragments connecting residues at the respective position. These
numbers are normalized such that regions of maximum similarity always
get a score of 9 - no matter how strong this maximum simliarity is. In
previous verions of the program, '*' characters were used instead of
numbers ; with the -stars=n option, '*' characters can be used as
previously.

<p>
At the bottom of the file you can find the "guide tree" used to make
the alignment, written in "nested parentheses" format.


<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: vtest.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;HTL2        
ldtapC-LFSDGSPQKAAYVLWDQTILQQDITPLPSHethsaqkgELLAliCglraAKPW
PSLNIFLDSKY-------------------------------------------------
-----------------------------------------
&gt;MMLV        
gkk---------------------------------------------------------
--LNVYTDSRYafatahihgeiyrrrglltsegkeiknkdeilallkalflpkrlsiihc
pghqkghsaeargnrmADQAARKAAITETPDTSTLL-----
&gt;HEPB        
rpgl-CqVFADATPTGWGLVMGHQRMRGTFSAPLPIHta------ELLAa-Cf---ARSR
SGANIIg-----------------------------------------------------
----------------TDNSGRTSLYADSPSVPSHLpdrvh
</pre>
</td></tr></table><p>
<p><h3>File: vtest.edialign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
 
                           DIALIGN 2.2.1 
                           *************
 
          Program code written by Burkhard Morgenstern and Said Abdeddaim 
             e-mail contact: dialign (at) gobics (dot) de 
 
          Published research assisted by DIALIGN 2 should cite:  
 
             Burkhard Morgenstern (1999).
             DIALIGN 2: improvement of the segment-to-segment
             approach to multiple sequence alignment.
             Bioinformatics 15, 211 - 218. 

          For more information, please visit the DIALIGN home page at 

             http://bibiserv.techfak.uni-bielefeld.de/dialign/ 
 
         ************************************************************
 


   program call:  edialign  

 
   Aligned sequences:          length:
   ==================          =======
 
   1) HTL2                        70
   2) MMLV                        97
   3) HEPB                        81

   Average seq. length:           82.7 


   Please note that only upper-case letters are considered to be aligned. 


   Alignment (DIALIGN format):
   ===========================
 
HTL2               1   ldtapC-LFS DGSPQKAAYV LWDQTILQQD ITPLPSHeth saqkgELLAl 
MMLV               1   gkk------- ---------- ---------- ---------- ---------- 
HEPB               1   rpgl-CqVFA DATPTGWGLV MGHQRMRGTF SAPLPIHta- -----ELLAa 
                                                                 
                       0000000999 9999999999 9999999999 9999999000 0000000000 
 
HTL2              50   iCglraAKPW PSLNIFLDSK Y--------- ---------- ---------- 
MMLV               4   ---------- --LNVYTDSR Yafatahihg eiyrrrgllt segkeiknkd 
HEPB              44   -Cf---ARSR SGANIIg--- ---------- ---------- ---------- 
                                                                 
                       0000000000 0077777777 7000000000 0000000000 0000000000 
 
HTL2              71   ---------- ---------- ---------- ---------- ---------- 
MMLV              42   eilallkalf lpkrlsiihc pghqkghsae argnrmADQA ARKAAITETP 
HEPB              57   ---------- ---------- ---------- ------TDNS GRTSLYADSP 
                                                                 
                       0000000000 0000000000 0000000000 0000001111 1111111111 
 
HTL2              71   ---------- - 
MMLV              92   DTSTLL---- - 
HEPB              71   SVPSHLpdrv h 
                       
                       1111110000 0 
 

 
 
   Sequence tree:
   ==============

Tree constructed using UPGMA based on DIALIGN fragment weight scores
 
((HTL2        :0.145587HEPB        :0.145587):0.108531MMLV        :0.254117);
 
 
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>


The scoring schemes are hard coded in the program and cannot be
changed. For proteins <b>edialign</b> always uses the BLOSUM62 table.


<H2>
    Notes
</H2>

We strongly recommend to use the "translation" option if nucleic acid
sequences are expected to contain protein coding regions, as it will
significantly increase the sensitivity of the alignment procedure in
such cases.

<p>
If you want to compare long genomic sequences it is recommended to
speed up the algorithm by:

<p>
<ul>
<li>
   setting "Nucleic acid sequence alignment mode" to "mixed alignment"
   (-nucmode=ma)
<li>
   setting "Maximum fragment length" to 30 (-lmax=30)
<li>
   setting "Consider only N-fragment pairs that start with two matches" to yes
   (-fragmat) and setting the similarity score threshold for considering
   P-fragment pairs to 8 (-fragsim=8) (which actually implies that you consider
   only fragments that start with a match).
<li>
   setting the "Threshold" T to 2.0 (-threshold=2.0)
</ul>

<p>
It is also recommended to increase the chance of finding coding exons
by setting "Nucleic acid sequence alignment mode" to "mixed alignment"
(-nucmode=ma) and setting "Also consider the reverse complement"
(-revcomp).


<H2>
    References
</H2>

<ol>

<li>
B. Morgenstern, A. Dress, T. Werner. Multiple DNA and protein sequence
alignment based on segment-to-segment
comparison. Proc. Natl. Acad. Sci.  USA 93, 12098 - 12103 (1996)

<li>
B. Morgenstern. DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment. Bioinformatics 15, 211 - 218
(1999).

<li>
B. Morgenstern, O. Rinner, S. Abdeddaim, D. Haase, K. F. X. Mayer,
A. W.  M. Dress H.-W. Mewes. Exon discovery by genomic sequence
alignment.  Bioinformatics 18, 777 - 787 (2002)

</ol>



<H2>
    Warnings
</H2>

Remember that lowercase characters represent parts of the sequence
that are not aligned. You should not use the dialign output as such
for sequence family or phylogeny studies, but take only part of the
alignment and/or remove the lowercase characters using a multiple
sequence editor. The current version of the program has no provision
for doing this automatically.


<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="emma.html">emma</a></td>
<td>Multiple sequence alignment (ClustalW wrapper)</td>
</tr>

<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>Display basic information about a multiple sequence alignment</td>
</tr>

<tr>
<td><a href="plotcon.html">plotcon</a></td>
<td>Plot conservation of a sequence alignment</td>
</tr>

<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Draw a sequence alignment with pretty formatting</td>
</tr>

<tr>
<td><a href="showalign.html">showalign</a></td>
<td>Display a multiple sequence alignment in pretty format</td>
</tr>

<tr>
<td><a href="tranalign.html">tranalign</a></td>
<td>Generate an alignment of nucleic coding regions from aligned proteins</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>
<!--
        Who has worked on the program in the past.
e.g. one of:
Alan Bleasby 
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
Bernd Jagla formerly at:
<br>
Cellular Biochemistry and Biophysics Program, Rockefeller
Research Laboratories, Memorial Sloan-Kettering Cancer Center, 1275 York
Avenue, Box 251,New York, NY 10021.

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
David Martin  

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Gos Micklem formerly at:
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
Ian Longden formerly at:
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.                      

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
Mark Faller formerly at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
Michael K. Schuster and Martin Grabner formerly at:
<br>
Austrian National EMBnet node.

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Michael Schmitz formerly at:
<br>
Lawrence Berkeley Labs, USA

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Nicolas Tourasse formerly at:
<br>
Biotechnology Center of Oslo

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Richard Durbin
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.                      

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Richard Bruskiewich formerly at:
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.                      

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Rodrigo Lopez
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Sinead O'Leary formerly at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK


<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
Tim Carver formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Thomas Laurent formerly at:
<br>
Lion Bioscience Ltd,
     Compass House,
     80-82 Newmarket Road,
     Cambridge,
     CB5 8DZ,
     UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.Val Curwen formerly at:
<br>
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK. 

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
   -->

The EMBOSS direct port was done by
Alan Bleasby 
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
based on ACD written by Guy Bottu (gbottu@ben.vub.ac.be) for a
wrapper written at BEN, ULB, Brussels, Belgium

<p>
The program DIALIGN itself was written by Burkhard Morgenstern, Said
Abdeddaim, Klaus Hahn, Thomas Werner, Kornelie Frech and Andreas
Dress.  Universitaet Bielefeld (FSPM and International Graduate School
in Bioinformatics and Genome Research) - GSF Research Center (ISG,
IBB, MIPS/IBI) - North Carolina State University - Universite de Rouen
- MPI fuer Biochemie (Martinsried) - University of Goettingen,
Institute of Microbiology and Genetics - Rhone-Poulenc Rorer

<p>
For help on the original DIALIGN2, contact: dialign@gobics.de

<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->
First committed on 5th December 2006.


<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


</BODY>
</HTML>