water.txt

emboss的linux版本的源代码

//

  Database entry: tsw:hbb_human

ID   HBB_HUMAN      STANDARD;      PRT;   146 AA.
AC   P02023;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   HEMOGLOBIN BETA CHAIN.
GN   HBB.
OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS   Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE.
RC   SPECIES=HUMAN;
RA   BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA   RUDLOFF V., WITTMANN-LIEBOLD B.;
RT   "The constitution of normal adult human haemoglobin.";
RL   Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 81064667.
RA   LAWN R.M., EFSTRATIADIS A., O'CONNELL C., MANIATIS T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   SEQUENCE OF 121-146 FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 85205333.
RA   LANG K.M., SPRITZ R.A.;
RT   "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT   segments.";
RL   Gene 33:191-196(1985).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC   SPECIES=HUMAN;
RX   MEDLINE; 76027820.
RA   FERMI G.;
RT   "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT   2.5-A resolution: refinement of the atomic model.";
RL   J. Mol. Biol. 97:237-256(1975).
RN   [5]
RP   SEQUENCE.
RC   SPECIES=P.TROGLODYTES;
RX   MEDLINE; 66071496.
RA   RIFKIN D.B., KONIGSBERG W.;
RT   "The characterization of the tryptic peptides from the hemoglobin of
RT   the chimpanzee (Pan troglodytes).";
RL   Biochim. Biophys. Acta 104:457-461(1965).
RN   [6]


  [Part of this file has been deleted for brevity]

FT   VARIANT     140    140       A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT                                /FTId=VAR_003081.
FT   VARIANT     140    140       A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT                                O2 AFFINITY UP).
FT                                /FTId=VAR_003082.
FT   VARIANT     141    141       L -> R (IN OLMSTED; UNSTABLE).
FT                                /FTId=VAR_003083.
FT   VARIANT     142    142       A -> D (IN OHIO; O2 AFFINITY UP).
FT                                /FTId=VAR_003084.
FT   VARIANT     143    143       H -> D (IN RANCHO MIRAGE).
FT                                /FTId=VAR_003085.
FT   VARIANT     143    143       H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT                                /FTId=VAR_003086.
FT   VARIANT     143    143       H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT                                /FTId=VAR_003087.
FT   VARIANT     143    143       H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT                                /FTId=VAR_003088.
FT   VARIANT     144    144       K -> E (IN MITO; O2 AFFINITY UP).
FT                                /FTId=VAR_003089.
FT   VARIANT     145    145       Y -> C (IN RAINIER; O2 AFFINITY UP).
FT                                /FTId=VAR_003090.
FT   VARIANT     145    145       Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT                                /FTId=VAR_003091.
FT   VARIANT     146    146       H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT                                /FTId=VAR_003092.
FT   VARIANT     146    146       H -> L (IN COWTOWN; O2 AFFINITY UP).
FT                                /FTId=VAR_003093.
FT   VARIANT     146    146       H -> P (IN YORK; O2 AFFINITY UP).
FT                                /FTId=VAR_003094.
FT   VARIANT     146    146       H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT                                /FTId=VAR_003095.
FT   HELIX         5     15
FT   TURN         16     17
FT   HELIX        20     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     55
FT   TURN         56     56
FT   HELIX        58     75
FT   TURN         76     77
FT   HELIX        78     94
FT   TURN         95     96
FT   TURN        100    100
FT   HELIX       101    121
FT   HELIX       124    142
FT   TURN        143    144
SQ   SEQUENCE   146 AA;  15867 MW;  EC9744C9 CRC32;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
//

Output file format

   The output is a standard EMBOSS alignment file.

   The results can be output in one of several styles by using the
   command-line qualifier -aformat xxx, where 'xxx' is replaced by the
   name of the required format. Some of the alignment formats can cope
   with an unlimited number of sequences, while others are only for pairs
   of sequences.

   The available multiple alignment format names are: unknown, multiple,
   simple, fasta, msf, trace, srs

   The available pairwise alignment format names are: pair, markx0,
   markx1, markx2, markx3, markx10, srspair, score

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

  Output files for usage example

  File: hba_human.water

########################################
# Program: water
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: water
#    [-asequence] tsw:hba_human
#    [-bsequence] tsw:hbb_human
# Align_format: srspair
# Report_file: hba_human.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 145
# Identity:      63/145 (43.4%)
# Similarity:    88/145 (60.7%)
# Gaps:           8/145 ( 5.5%)
# Score: 293.5
#
#
#=======================================

HBA_HUMAN          2 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-     49
                     |:|.:|:.|.|.||||  :..|.|.|||.|:.:.:|.|:.:|..| |||
HBB_HUMAN          3 LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST     50

HBA_HUMAN         50 ----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP     95
                         .|:.:||.|||||..|.::.:||:|::....:.||:||..||.|||
HBB_HUMAN         51 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP    100

HBA_HUMAN         96 VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY    140
                     .||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||
HBB_HUMAN        101 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY    145


#---------------------------------------
#---------------------------------------

   The Identity: is the percentage of identical matches between the two
   sequences over the reported aligned region (including any gaps in the
   length).

   The Similarity: is the percentage of matches between the two sequences
   over the reported aligned region (including any gaps in the length).

Data files

   For protein sequences EBLOSUM62 is used for the substitution matrix.
   For nucleotide sequence, EDNAFULL is used. Others can be specified.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   water is a true implementation of the Smith-Waterman algorithm and so
   produces a full path matrix. It therefore cannot be used with genome
   sized sequences unless you have a lot of memory and a lot of time.

References

    1. Smith TF, Waterman MS (1981) J. Mol. Biol 147(1);195-7

Warnings

   Local alignment methods only report the best matching areas between
   two sequences - there may be a large number of alternative local
   alignments that do not score as highly. If two proteins share more
   than one common region, for example one has a single copy of a
   particular domain while the other has two copies, it may be possible
   to "miss" the second and subsequent alignments. You will be able to
   see this situation if you have done a dotplot and your local alignment
   does not show all the features you expected to see.

   water is for aligning the best matching subsequences of two sequences.
   It does not necessarily align whole sequences against each other; you
   should use needle if you wish to align closely related sequences along
   their whole lengths.

   A true Smith Waterman implementation like water needs memory
   proportional to the product of the sequence lengths. For two sequences
   of length 10,000,000 and 1,000 it therefore needs memory proportional
   to 10,000,000,000 characters. Two arrays of this size are produced,
   one of ints and one of floats so multiply that figure by 8 to get the
   memory usage in bytes. That doesn't include other overheads. Therefore
   only use water and needle for accurate alignment of reasonably short
   sequences.

   If you run out of memory, try using supermatcher or matcher.

Diagnostic Error Messages

Uncaught exception
 Assertion failed
 raised at ajmem.c:xxx

   Probably means you have run out of memory. Try using supermatcher or
   matcher if this happens.

Exit status

   0 if successful.

Known bugs

   None.

See also

   Program name                         Description
   matcher      Finds the best local alignments between two sequences
   seqmatchall  All-against-all comparison of a set of sequences
   supermatcher Match large sequences against one or more other sequences
   wordfinder   Match large sequences against one or more other sequences
   wordmatch    Finds all exact matches of a given size between 2 sequences

   matcher is a local alignment program that gives as good an alignment
   as

   water
   but it uses far less memory. However,

   water
   runs twice as fast as matcher.

   supermatcher is designed for local alignments of very large sequences.
   It gives good results as long as there is not significant amounts of
   insertion or deletion in the alignment.

   supermatcher Finds a match of a large sequence against one or more
   sequences matcher Finds the best local alignments between two
   sequences

Author(s)

   Alan Bleasby (ajb