                                  edialign



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Function

   Local multiple alignment of sequences

Description

   edialign 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, edialign 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.

Algorithm

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

   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.

   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.

   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.

   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".

   For the levels of sequence similarity, release 2.2 of DIALIGN has two
   additional options:
     * 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.
     * 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".

   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.

Usage

   Here is a sample session with edialign


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


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

Command line arguments

Local multiple alignment of sequences
Version: EMBOSS:6.5.6.0

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


Input file format

   edialign reads nucleotide or protein sequences to be aligned.

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

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

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

   The input format can be specified by using the command-line qualifier
   -sformat xxx, 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.

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

  Input files for usage example

  File: vtest.seq

>HTL2
LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAKPWP
SLNIFLDSKY
>MMLV
GKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIH
CPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL
>HEPB
RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNS
GRTSLYADSPSVPSHLPDRVH

Output file format

   edialign 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).

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

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

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

   The input format can be specified by using the command-line qualifier
   -sformat xxx, 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.

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

   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.

   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.

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

  Output files for usage example

  File: vtest.fasta

>HTL2
ldtapC-LFSDGSPQKAAYVLWDQTILQQDITPLPSHethsaqkgELLAliCglraAKPW
PSLNIFLDSKY-------------------------------------------------
-----------------------------------------
>MMLV
gkk---------------------------------------------------------
--LNVYTDSRYafatahihgeiyrrrglltsegkeiknkdeilallkalflpkrlsiihc
pghqkghsaeargnrmADQAARKAAITETPDTSTLL-----
>HEPB
rpgl-CqVFADATPTGWGLVMGHQRMRGTFSAPLPIHta------ELLAa-Cf---ARSR
SGANIIg-----------------------------------------------------
----------------TDNSGRTSLYADSPSVPSHLpdrvh

  File: vtest.edialign


                           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);



Data files

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

Notes

   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.

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

     * setting "Nucleic acid sequence alignment mode" to "mixed alignment"
       (-nucmode=ma)
     * setting "Maximum fragment length" to 30 (-lmax=30)
     * 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).
     * setting the "Threshold" T to 2.0 (-threshold=2.0)

   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).

References

    1. 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)
    2. B. Morgenstern. DIALIGN 2: improvement of the segment-to-segment
       approach to multiple sequence alignment. Bioinformatics 15, 211 -
       218 (1999).
    3. 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)

Warnings

   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.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   emma             Multiple sequence alignment (ClustalW wrapper)
   infoalign        Display basic information about a multiple sequence alignment
   plotcon          Plot conservation of a sequence alignment
   prettyplot       Draw a sequence alignment with pretty formatting
   showalign        Display a multiple sequence alignment in pretty format
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins

Author(s)

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

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) 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

   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

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

History

   First committed on 5th December 2006.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
