edialign.txt

emboss的linux版本的源代码

  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). 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 alignment program - interface to ClustalW program
   infoalign    Information on a multiple sequence alignment
   plotcon      Plot quality of conservation of a sequence alignment
   prettyplot   Displays aligned sequences, with colouring and boxing
   showalign    Displays a multiple sequence alignment
   tranalign    Align nucleic coding regions given the aligned proteins

Author(s)

   The EMBOSS direct port was done by Alan Bleasby (ajb