edialign |
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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:
% 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
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Local multiple alignment of sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequences] seqset Sequence set filename and optional format, or reference (input USA) [-outfile] outfile [*.edialign] Output file name [-outseq] seqoutall [ |
Qualifier | Type | Description | Allowed values | Default | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||
[-sequences] (Parameter 1) |
seqset | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||
[-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.edialign | ||||||
[-outseq] (Parameter 3) |
seqoutall | (Aligned) sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format | ||||||
Additional (Optional) qualifiers | ||||||||||
-nucmode | list | Nucleic acid sequence alignment mode (simple, translated or mixed) |
|
n | ||||||
-revcomp | boolean | Also consider the reverse complement | Boolean value Yes/No | No | ||||||
-overlapw | selection | By default overlap weights are used when Nseq =<35 but you can set this to 'yes' or 'no' | Choose from selection list of values | default (when Nseq =< 35) | ||||||
-linkage | list | Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage) |
|
UPGMA | ||||||
-maxfragl | integer | Maximum fragment length | Integer 0 or more | 40 | ||||||
-fragmat | boolean | Consider only N-fragment pairs that start with two matches | Boolean value Yes/No | No | ||||||
-fragsim | integer | Consider only P-fragment pairs if first amino acid or codon pair has similarity score of at least n | Integer 0 or more | 4 | ||||||
-itscore | boolean | Use iterative score | Boolean value Yes/No | No | ||||||
-threshold | float | Threshold for considering diagonal for alignment | Number 0.000 or more | 0.0 | ||||||
Advanced (Unprompted) qualifiers | ||||||||||
-mask | boolean | Replace unaligned characters by stars '*' rather then putting them in lowercase | Boolean value Yes/No | No | ||||||
-dostars | boolean | Activate writing of stars instead of numbers | Boolean value Yes/No | No | ||||||
-starnum | integer | Put up to n stars '*' instead of digits 0-9 to indicate level of conservation | Integer 0 or more | 4 | ||||||
Associated qualifiers | ||||||||||
"-sequences" associated seqset qualifiers | ||||||||||
-sbegin1 -sbegin_sequences |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||
-send1 -send_sequences |
integer | End of each sequence to be used | Any integer value | 0 | ||||||
-sreverse1 -sreverse_sequences |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
-sask1 -sask_sequences |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
-snucleotide1 -snucleotide_sequences |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
-sprotein1 -sprotein_sequences |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
-slower1 -slower_sequences |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
-supper1 -supper_sequences |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
-sformat1 -sformat_sequences |
string | Input sequence format | Any string | |||||||
-sdbname1 -sdbname_sequences |
string | Database name | Any string | |||||||
-sid1 -sid_sequences |
string | Entryname | Any string | |||||||
-ufo1 -ufo_sequences |
string | UFO features | Any string | |||||||
-fformat1 -fformat_sequences |
string | Features format | Any string | |||||||
-fopenfile1 -fopenfile_sequences |
string | Features file name | Any string | |||||||
"-outfile" associated outfile qualifiers | ||||||||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||
"-outseq" associated seqoutall qualifiers | ||||||||||
-osformat3 -osformat_outseq |
string | Output seq format | Any string | |||||||
-osextension3 -osextension_outseq |
string | File name extension | Any string | |||||||
-osname3 -osname_outseq |
string | Base file name | Any string | |||||||
-osdirectory3 -osdirectory_outseq |
string | Output directory | Any string | |||||||
-osdbname3 -osdbname_outseq |
string | Database name to add | Any string | |||||||
-ossingle3 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||
-oufo3 -oufo_outseq |
string | UFO features | Any string | |||||||
-offormat3 -offormat_outseq |
string | Features format | Any string | |||||||
-ofname3 -ofname_outseq |
string | Features file name | Any string | |||||||
-ofdirectory3 -ofdirectory_outseq |
string | Output directory | Any string | |||||||
General qualifiers | ||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
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.
>HTL2 LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAKPWP SLNIFLDSKY >MMLV GKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIH CPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL >HEPB RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNS GRTSLYADSPSVPSHLPDRVH |
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.
>HTL2 ldtapC-LFSDGSPQKAAYVLWDQTILQQDITPLPSHethsaqkgELLAliCglraAKPW PSLNIFLDSKY------------------------------------------------- ----------------------------------------- >MMLV gkk--------------------------------------------------------- --LNVYTDSRYafatahihgeiyrrrglltsegkeiknkdeilallkalflpkrlsiihc pghqkghsaeargnrmADQAARKAAITETPDTSTLL----- >HEPB rpgl-CqVFADATPTGWGLVMGHQRMRGTFSAPLPIHta------ELLAa-Cf---ARSR SGANIIg----------------------------------------------------- ----------------TDNSGRTSLYADSPSVPSHLpdrvh |
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); |
If you want to compare long genomic sequences it is recommended to speed up the algorithm by:
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).
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © 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