stretcher.txt

emboss的linux版本的源代码

                                 stretcher 



Function

   Finds the best global alignment between two sequences

Description

   stretcher calculates a global alignment of two sequences using a
   modification of the classic dynamic programming algorithm which uses
   linear space.

   A global pairwise alignment is one where it is assumed that the two
   sequences have diverged from a common ancestor and that the program
   should try to stretch the two sequences, introducing gaps where
   necessary, in order to show the alignment over the whole length of the
   two sequences that best illustrates their similarities.

   In contrast, a local alignment program like matcher simply finds
   local, small parts of the two sequences where there is some similarity
   and makes no assumption about the whole length of the sequence needing
   to be similar.

   The standard sequence global alignment program using the Needleman &
   Wunsch algorithm, as implemented in the program needle, requires O(MN)
   space and O(N) time. This is standard computer-science language for it
   needing an amount of computer memory that is proportional to the
   product of the two sequences being aligned and taking an amount of
   time that is proportional to the shorter of the two sequences. So if a
   1 kb and a 10 kb sequence take 10 Mega-words of memory and 10 minutes
   to align, you should expect that in order to align a 10 kb sequence
   and a 1 Mb sequence you will need appoximately 10 Giga-words of memory
   and 100 minutes. Computer memory will rapidly be exhausted as the size
   of the aligned sequences increases.

   This program implements the Myers and Miller algorithm for finding an
   optimal global alignment in an amount of computer memory that is only
   proportional to the size of the smaller sequence - O(N).

   In computing, a benefit is seldom gained without a cost elsewhere. The
   cost of gaining a memory-efficient alignment is that it takes about
   twice the amount of time to do the alignment as the Needleman & Wunsch
   algorithm. In computer-science language the time is approximately
   O(2N).

Usage

   Here is a sample session with stretcher


% stretcher tsw:hba_human tsw:hbb_human 
Finds the best global alignment between two sequences
Output alignment [hba_human.stretcher]: 

   Go to the input files for this example
   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      [*.stretcher] 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.
   -gapopen            integer    [12 for protein, 16 for nucleic] Gap penalty
                                  (Positive integer)
   -gapextend          integer    [2 for protein, 4 for nucleic] Gap length
                                  penalty (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

   stretcher reads 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