matcher.txt

emboss的linux版本的源代码

                                  matcher 



Function

   Finds the best local alignments between two sequences

Description

   matcher compares two sequences looking for local sequence similarities
   using a rigorous algorithm.

   matcher is based on Bill Pearson's 'lalign' application, version 2.0u4
   Feb. 1996

   Lalign uses code developed by X. Huang and W. Miller (Adv. Appl. Math.
   (1991) 12:337-357) for the "sim" program, which is a linear-space
   version of an algorithm described by M. S. Waterman and M. Eggert (J.
   Mol. Biol. 197:723-728).

   Like water, matcher is rigorous, but also very slow. The advantage of
   matcher is that it uses far less memory than water, so you are much
   less likely to run out of memory when aligning large sequences.

   matcher will also report a specified number of alignments between the
   two sequences showing the actual local alignments. (water will only
   report the single best match.) The default number of alignments output
   is 1, but can be increased to (for example) the 10 best alignments by
   using the '-alternatives 10' command-line qualifier. In some cases,
   for example multidomain proteins or cDNA and genomic DNA comparisons,
   there may be many interesting and significant alignments.

Usage

   Here is a sample session with matcher


% matcher tsw:hba_human tsw:hbb_human 
Finds the best local alignments between two sequences
Output alignment [hba_human.matcher]: 

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

   Example 2

   To find the 10 best alignments:


% matcher tsw:hba_human tsw:hbb_human -alt 10 
Finds the best local alignments between two sequences
Output alignment [hba_human.matcher]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-outfile]           align      [*.matcher] Output alignment file name

   Additional (Optional) qualifiers:
   -datafile           matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -alternatives       integer    [1] This sets the number of alternative
                                  matches output. By default only the highest
                                  scoring alignment is shown. A value of 2
                                  gives you other reasonable alignments. In
                                  some cases, for example multidomain proteins
                                  of cDNA and genomic DNA comparisons, there
                                  may be other interesting and significant
                                  alignments. (Integer 1 or more)
   -gapopen            integer    [14 for protein, 16 for nucleic] The gap
                                  penalty is the score taken away when a gap
                                  is created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value of 14 assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, or a
                                  value of 16 and the EDNAFULL matrix for
                                  nucleotide sequences. (Positive integer)
   -gapextend          integer    [4 for any sequence] The gap length, or gap
                                  extension, penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. An exception is where one or
                                  both sequences are single reads with
                                  possible sequencing errors in which case you
                                  would expect many single base gaps. You can
                                  get this result by setting the gap penalty
                                  to zero (or very low) and using the gap
                                  extension penalty to control gap scoring.
                                  (Positive integer)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -aformat3           string     Alignment format
   -aextension3        string     File name extension
   -adirectory3        string     Output directory
   -aname3             string     Base file name
   -awidth3            integer    Alignment width
   -aaccshow3          boolean    Show accession number in the header
   -adesshow3          boolean    Show description in the header
   -ausashow3          boolean    Show the full USA in the alignment
   -aglobal3           boolean    Show the full sequence in alignment

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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

Input file format

   matcher reads in any 2 sequence USAs of the same type (DNA or
   protein).

  Input files for usage example

   'tsw:hba_human' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:hba_human

ID   HBA_HUMAN      STANDARD;      PRT;   141 AA.
AC   P01922;
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 ALPHA CHAIN.
GN   HBA1 AND HBA2.
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 FROM N.A. (ALPHA-1).
RX   MEDLINE; 81088339.
RA   MICHELSON A.M., ORKIN S.H.;
RT   "The 3' untranslated regions of the duplicated human alpha-globin
RT   genes are unexpectedly divergent.";
RL   Cell 22:371-377(1980).
RN   [2]
RP   SEQUENCE FROM N.A. (ALPHA-2).
RX   MEDLINE; 81175088.
RA   LIEBHABER S.A., GOOSSENS M.J., KAN Y.W.;
RT   "Cloning and complete nucleotide sequence of human 5'-alpha-globin
RT   gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
RN   [3]
RP   SEQUENCE FROM N.A. (ALPHA-2).
RX   MEDLINE; 80137531.
RA   WILSON J.T., WILSON L.B., REDDY V.B., CAVALLESCO C., GHOSH P.K.,
RA   DERIEL J.K., FORGET B.G., WEISSMAN S.M.;
RT   "Nucleotide sequence of the coding portion of human alpha globin
RT   messenger RNA.";
RL   J. Biol. Chem. 255:2807-2815(1980).
RN   [4]
RP   SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).
RA   FLINT J., HIGGS D.R.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   SEQUENCE.
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   [6]
RP   SEQUENCE.
RA   HILL R.J., KONIGSBERG W.;
RT   "The structure of human hemoglobin: IV. The chymotryptic digestion of
RT   the alpha chain of human hemoglobin.";
RL   J. Biol. Chem. 237:3151-3156(1962).
RN   [7]


  [Part of this file has been deleted for brevity]

FT                                /FTId=VAR_002841.
FT   VARIANT     130    130       A -> D (IN YUDA; O2 AFFINITY DOWN).
FT                                /FTId=VAR_002842.
FT   VARIANT     131    131       S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE;
FT                                CAUSES ALPHA-THALASSEMIA).
FT                                /FTId=VAR_002843.
FT   VARIANT     133    133       S -> R (IN VAL DE MARNE; O2 AFFINITY UP).
FT                                /FTId=VAR_002844.
FT   VARIANT     135    135       V -> E (IN PAVIE).
FT                                /FTId=VAR_002845.
FT   VARIANT     136    136       L -> M (IN CHICAGO).
FT                                /FTId=VAR_002846.
FT   VARIANT     136    136       L -> P (IN BIBBA; UNSTABLE;
FT                                CAUSES ALPHA-THALASSEMIA).
FT                                /FTId=VAR_002847.
FT   VARIANT     138    138       S -> P (IN ATTLEBORO; O2 AFFINITY UP).
FT                                /FTId=VAR_002848.
FT   VARIANT     139    139       K -> E (IN HANAKAMI; O2 AFFINITY UP).
FT                                /FTId=VAR_002849.
FT   VARIANT     139    139       K -> T (IN TOKONAME; O2 AFFINITY UP).
FT                                /FTId=VAR_002850.
FT   VARIANT     140    140       Y -> H (IN ROUEN; O2 AFFINITY UP).
FT                                /FTId=VAR_002851.
FT   VARIANT     141    141       R -> C (IN NUNOBIKI; O2 AFFINITY UP).
FT                                /FTId=VAR_002852.
FT   VARIANT     141    141       R -> L (IN LEGNANO; O2 AFFINITY UP).
FT                                /FTId=VAR_002853.
FT   VARIANT     141    141       R -> H (IN SURESNES; O2 AFFINITY UP).
FT                                /FTId=VAR_002854.
FT   VARIANT     141    141       R -> P (IN SINGAPORE).
FT                                /FTId=VAR_002855.
FT   HELIX         4     35
FT   HELIX        37     42
FT   TURN         44     45
FT   TURN         50     51
FT   HELIX        53     71
FT   TURN         72     74
FT   HELIX        76     79
FT   TURN         80     80
FT   HELIX        81     89
FT   TURN         90     91
FT   TURN         95     95
FT   HELIX        96    112
FT   TURN        114    116
FT   HELIX       119    136
FT   TURN        137    139
SQ   SEQUENCE   141 AA;  15126 MW;  5EC7DB1E CRC32;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
//

  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.