emma.txt

emboss的linux版本的源代码

   '.pep', type:

   ls *.pep > listfile

  Several sequences in one file

   EMBOSS can read in a single file which contains many sequences.

   Each of the sequences in the file must be in the same format - if the
   first sequence is in EMBL format, then all the others must be in EMBL
   format.

   There are some sequence formats that cannot be used when placing many
   sequences in the same file. These are sequence formats that have no
   clear indication of where the sequence ends and the annotation of the
   next sequence starts. These formats include: plain or text format (no
   real format, just the sequence), staden, gcg.

   If your sequences are not already in a single file, you can place them
   in one using seqret. The following example takes all the files ending
   in '.pep' and places them in the file 'mystuff' in Fasta format.

   seqret "*.pep" mystuff

   When emma asks for the sequences to align, you should type 'mystuff'.

  Using wildcards

   'Wildcard' characters are characters that are expanded to match all
   possible matching files or entries in a database.

   By far the most commonly used wildcard character is '*' which matches
   any number (or zero) of possible characters at that position in the
   name.

   A less commonly used wildcard character is '?' which matches any one
   character at that position.

   For example, when emma asks for sequences to align, you could answer:
   abc*.pep This would select any files whose name starts with 'abc' and
   then ends in '.pep'; the centre of the name where there is a '*' can
   be anything.

   Both file names and database entry names can be wildcarded.

   There is a slightly irritating problem that occurs when wildcards are
   used one the Unix command line (This is the line that you type against
   the 'Unix' prompt together with the program name.)

   In this case the Unix session gets the command line first, runs the
   program, expands the wildcards and passes the program parameters to
   the program. When Unix expands the wildcards, two things go wrong. You
   may have specified wildcarded database entries - the Unix system tries
   to file files that match that specification, it fails and refuses to
   run the program. Alternatively, you may have specified wildcarded
   files - Unix fileds them and gives the name of each of them to the
   program as a separate parameter - emma gets the wrong number of
   parameters and refuses to run.

   You get round this by quoting the wildcard. You can either put the
   whole wildcarded name in quotes:
   "abc*.pep"
   or you can quote just the '*' using a '\' as:
   abc\*.pep

   This problem does not occur when you reply to the prompt from the
   program for the input sequences, or when you are typing the wildcard
   files name in a web browser of GUI (such as Jemboss or SPIN) field

Output file format

  Output files for usage example

  File: hbb_human.aln

>HBB_HUMAN
--------VHLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP----ENFRLL
GNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
>HBB_HORSE
--------VQLSGEEKAAVLALWDKVN--EEEVGGEALGRLLVVYPWTQRFFDSFGDLSN
PGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDP----ENFRLL
GNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH------
>HBA_HUMAN
---------VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-----
-DLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP----VNFKLL
SHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
>HBA_HORSE
---------VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHF-----
-DLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDP----VNFKLL
SHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR------
>MYG_PHYCA
---------VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
EAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPI----KYLEFI
SEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQ----VDPQYF
KVLAAVIADTVAAGDAGFEKLMSMICILLRSAY-------------
>LGB2_LUPLU
--------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKG--T
SEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVV
KEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA---

  File: hbb_human.dnd

(
(
(
(
HBB_HUMAN:0.08080,
HBB_HORSE:0.08359)
:0.21952,
(
HBA_HUMAN:0.05452,
HBA_HORSE:0.06605)
:0.21070)
:0.06034,
MYG_PHYCA:0.39882)
:0.01490,
GLB5_PETMA:0.38267,
LGB2_LUPLU:0.50324);

  Sequences

   emma writes the aligned sequences and a dendrogram file showing how
   the sequences were clustered during the progressive alignments.

   The clustalw output sequences are reformatted into the default EMBOSS
   output format instead of being left as Clustal-format '.aln' files.

  Trees

   Believe it or not, we now use the New Hampshire (nested parentheses)
   format as default for our trees. This format is compatible with e.g.
   the PHYLIP package. If you want to view a tree, you can use the RETREE
   or DRAWGRAM/DRAWTREE programs of PHYLIP. This format is used for all
   our trees, even the initial guide trees for deciding the order of
   multiple alignment. The output trees from the phylogenetic tree menu
   can also be requested in our old verbose/cryptic format. This may be
   more useful if, for example, you wish to see the bootstrap figures.
   The bootstrap trees in the default New Hampshire format give the
   bootstrap figures as extra labels which can be viewed very easily
   using TREETOOL which is available as part of the GDE package. TREETOOL
   is available from the RDP project by ftp from rdp.life.uiuc.edu.

   The New Hampshire format is only useful if you have software to
   display or manipulate the trees. The PHYLIP package is highly
   recommended if you intend to do much work with trees and includes
   programs for doing this. WE DO NOT PROVIDE ANY DIRECT MEANS FOR
   VIEWING TREES GRAPHICALLY.

Data files

   The comparison matrices available for clustalw are not EMBOSS matrix
   files, as they are defined in the clustalw code. The matrices
   available for carrying out a protein sequence alignment are:
     * blosum
     * pam
     * gonnet
     * id
     * user defined

   The comparison matrices available in clustalw for carrying out a
   nucleotide sequence alignment are:
     * iub
     * clustalw
     * user defined

Notes

   None

References

   The main reference for ClustalW is Thompson et al below.
    1. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) "CLUSTAL W:
       improving the sensitivity of progressive multiple sequence
       alignment through sequence weighting, positions-specific gap
       penalties and weight matrix choice." Nucleic Acids Research,
       22:4673-4680.
    2. Feng, D.-F. and Doolittle, R.F. (1987). J. Mol. Evol. 25, 351-360.
    3. Needleman, S.B. and Wunsch, C.D. (1970). J. Mol. Biol. 48,
       443-453.
    4. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) in Atlas of
       Protein Sequence and Structure, vol. 5, suppl. 3 (Dayhoff, M.O.,
       ed.), pp 345-352, NBRF, Washington.
    5. Henikoff, S. and Henikoff, J.G. (1992). Proc. Natl. Acad. Sci. USA
       89, 10915-10919.
    6. Lipman, D.J., Altschul, S.F. and Kececioglu, J.D. (1989). Proc.
       Natl. Acad. Sci. USA 86, 4412-4415.
    7. Barton, G.J. and Sternberg, M.J.E. (1987). J. Mol. Biol. 198,
       327-337.
    8. Gotoh, O. (1993). CABIOS 9, 361-370.
    9. Altschul, S.F. (1989). J. Theor. Biol. 138, 297-309.
   10. Lukashin, A.V., Engelbrecht, J. and Brunak, S. (1992). Nucl. Acids
       Res. 20, 2511-2516.
   11. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald,
       A.F. and Wooton, J.C. (1993). Science, 262, 208-214.
   12. Vingron, M. and Waterman, M.S. (1993). J. Mol. Biol. 234, 1-12.
   13. Pascarella, S. and Argos, P. (1992). J. Mol. Biol. 224, 461-471.
   14. Collins, J.F. and Coulson, A.F.W. (1987). In Nucleic acid and
       protein sequence analysis a practical approach, Bishop, M.J. and
       Rawlings, C.J. ed., chapter 13, pp. 323-358.
   15. Vingron, M. and Sibbald, P.R. (1993). Proc. Natl. Acad. Sci. USA,
       90, 8777-8781.
   16. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994). CABIOS, 10,
       19-29.
   17. Lthy, R., Xenarios, I. and Bucher, P. (1994). Protein Science, 3,
       139-146.
   18. Higgins, D.G. and Sharp, P.M. (1988). Gene, 73, 237-244.
   19. Higgins, D.G. and Sharp, P.M. (1989). CABIOS, 5, 151-153.
   20. Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992). CABIOS, 8,
       189-191.
   21. Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy, W.H.
       Freeman, San Francisco.
   22. Saitou, N. and Nei, M. (1987). Mol. Biol. Evol. 4, 406-425.
   23. Wilbur, W.J. and Lipman, D.J. (1983). Proc. Natl. Acad. Sci. USA,
       80, 726-730.
   24. Musacchio, A., Gibson, T., Lehto, V.-P. and Saraste, M. (1992).
       FEBS Lett. 307, 55-61.
   25. Musacchio, A., Noble, M., Pauptit, R., Wierenga, R. and Saraste,
       M. (1992). Nature, 359, 851-855.
   26. Bashford, D., Chothia, C. and Lesk, A.M. (1987). J. Mol. Biol.
       196, 199-216.
   27. Myers, E.W. and Miller, W. (1988). CABIOS, 4, 11-17.
   28. Thompson, J.D. (1994). CABIOS, (Submitted).
   29. Smith, T.F., Waterman, M.S. and Fitch, W.M. (1981). J. Mol. Evol.
       18, 38-46.
   30. Pearson, W.R. and Lipman, D.J. (1988). Proc. Natl. Acad. Sci. USA.
       85, 2444-2448.
   31. Devereux, J., Haeberli, P. and Smithies, O. (1984). Nucleic Acids
       Res. 12, 387-395.
   32. Felsenstein, J. (1989). Cladistics 5, 164-166.
   33. Kimura, M. (1980). J. Mol. Evol. 16, 111-120.
   34. Kimura, M. (1983). The Neutral Theory of Molecular Evolution.
       Cambridge University Press, Cambridge.
   35. Felsenstein, J. (1985). Evolution 39, 783-791.
   36. Smith, R.F. and Smith, T.F. (1992) Protein Engineering 5, 35-41.
   37. Krogh, A., Brown, M., Mian, S., Sjlander, K. and Haussler, D.
       (1994) J. Mol. Biol. 235-1501-1531.
   38. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1994). FEBS Lett.
       339, 269-275.
   39. Bairoch, A. and Bckmann, B. (1992) Nucleic Acids Res., 20,
       2019-2022.
   40. Noble, M.E.M., Musacchio, A., Saraste, M., Courtneidge, S.A. and
       Wierenga, R.K. (1993) EMBO J. 12, 2617-2624.
   41. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.

Warnings

   None.

Diagnostic Error Messages

   "cannot find program 'clustalw'" - means that the ClustalW program has
   not been set up on your site or is not in your environment (i.e. is
   not on your path). The solutions are to (1) install clustalw in the
   path so that emma can find it with the command "clustalw", or (2)
   define a variable (an environment variable of in emboss.defaults or
   your .embossrc file) called EMBOSS_CLUSTALW containing the command
   (program name or full path) to run clustalw if you have it elsewhere
   on your system.

Exit status

   It exits with status 0 unless an error is reported

Known bugs

   None.

See also

   Program name                       Description
   edialign     Local multiple alignment of sequences
   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)

   Mark Faller (current e-mail address unknown)
   while he was with:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Completed 18 February 1999

Target users

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

Comments

   None