emowse.txt

emboss的linux版本的源代码

          2424.7
          2930.3
          3086.3
          5423.0
          6082.8

1   100K_RAT     100 KDA PROTEIN (EC 6.3.2.-).
2   SYV_FUGRU    VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALR
3   TCPD_FUGRU   T-COMPLEX PROTEIN 1, DELTA SUBUNIT (TCP-1-DELTA) (CCT-DELTA).
4   FLAV_ECOLI   FLAVODOXIN 1.
5   OPS2_DROME   OPSIN RH2 (OCELLAR OPSIN).
6   FLAV_KLEPN   FLAVODOXIN.
7   FLAV_SYNY3   FLAVODOXIN.
8   E2BB_FUGRU   TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GDP-
9   FLAV_HAEIN   FLAVODOXIN.
10  HIRA_FUGRU   HIRA PROTEIN (TUP1 LIKE ENHANCER OF SPLIT PROTEIN 1).
11  OPS2_SCHGR   OPSIN 2.
12  HBA_HUMAN    HEMOGLOBIN ALPHA CHAIN.
13  LACY_ECOLI   LACTOSE PERMEASE (LACTOSE-PROTON SYMPORT).
14  FLAV_CLOAB   FLAVODOXIN.
15  PAX3_HUMAN   PAIRED BOX PROTEIN PAX-3 (HUP2).
16  PAX4_HUMAN   PAIRED BOX PROTEIN PAX-4.
17  CO9_FUGRU    COMPLEMENT COMPONENT C9 PRECURSOR.
18  SYH_FUGRU    HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE
19  BGAL_ECOLI   BETA-GALACTOSIDASE (EC 3.2.1.23) (LACTASE).
20  HD_FUGRU     HUNTINGTIN (HUNTINGTON'S DISEASE PROTEIN HOMOLOG) (HD PROTEIN)

    1  : 100K_RAT       1.277e+06 100368.6   0.750
         100 KDA PROTEIN (EC 6.3.2.-).
         Mw     Start  End    Seq
         1086.3 358    367    CATTPMAVHR
         1399.6 6      17     GDFLNYALSLMR
         2424.7 290    312    VFMEDVGAEPGSILTELGGFEVK
         2930.3 671    698    QLILASQSSDADAVFSAMDLAFAVDLCK
         3086.3 458    485    QLSIDTRPFRPASEGNPSDDPDPLPAHR
        *6082.8 817    870    QDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISR...
         No Match      2030.2 5423.0

    2  : SYV_FUGRU      3.791e+01 138217.9   0.375
         VALYL-TRNA SYNTHETASE (EC 6.1.1.9) (VALINE--TRNA LIGASE) (VALRS).
         Mw     Start  End    Seq
         1087.3 510    518    TVLHPFCDR
        *1399.6 1184   1195   VPVKVQEQDTEK
         2425.7 321    343    GETTLWNPGCDHAGIATQVVVEK
         No Match      2030.2 2930.3 3086.3 5423.0 6082.8


  [Part of this file has been deleted for brevity]

         No Match      1399.6 2030.2 2424.7 2930.3 3086.3 5423.0 6082.8

    13 : LACY_ECOLI     5.070e+00 46503.1    0.125
         LACTOSE PERMEASE (LACTOSE-PROTON SYMPORT).
         Mw     Start  End    Seq
        *3088.7 290    319    NALLLAGTIMSVRIIGSSFATSALEVVILK
         No Match      1086.2 1399.6 2030.2 2424.7 2930.3 5423.0 6082.8

    14 : FLAV_CLOAB     4.938e+00 17763.3    0.125
         FLAVODOXIN.
         Mw     Start  End    Seq
        *1085.3 17     26     VAKLIEEGVK
         No Match      1399.6 2030.2 2424.7 2930.3 3086.3 5423.0 6082.8

    15 : PAX3_HUMAN     3.494e+00 52967.4    0.125
         PAIRED BOX PROTEIN PAX-3 (HUP2).
         Mw     Start  End    Seq
        *2930.3 11     37     MMRPGPGQNYPRSGFPLEVSTPLGQGR
         No Match      1086.2 1399.6 2030.2 2424.7 3086.3 5423.0 6082.8

    16 : PAX4_HUMAN     3.488e+00 37832.6    0.125
         PAIRED BOX PROTEIN PAX-4.
         Mw     Start  End    Seq
        *2029.4 28     45     QQIVRLAVSGMRPCDISR
         No Match      1086.2 1399.6 2424.7 2930.3 3086.3 5423.0 6082.8

    17 : CO9_FUGRU      3.007e+00 65197.8    0.125
         COMPLEMENT COMPONENT C9 PRECURSOR.
         Mw     Start  End    Seq
        *2930.2 135    162    TCPPTVLDTNEQGRTAGYGINILGADPR
         No Match      1086.2 1399.6 2030.2 2424.7 3086.3 5423.0 6082.8

    18 : SYH_FUGRU      2.821e+00 57912.8    0.125
         HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS
).
         Mw     Start  End    Seq
         1087.2 124    133    DQGGELLSLR
         No Match      1399.6 2030.2 2424.7 2930.3 3086.3 5423.0 6082.8

    19 : BGAL_ECOLI     2.283e+00 116351.4   0.125
         BETA-GALACTOSIDASE (EC 3.2.1.23) (LACTASE).
         Mw     Start  End    Seq
         1400.6 600    611    QFCMNGLVFADR
         No Match      1086.2 2030.2 2424.7 2930.3 3086.3 5423.0 6082.8

    20 : HD_FUGRU       2.169e+00 348935.6   0.375
         HUNTINGTIN (HUNTINGTON'S DISEASE PROTEIN HOMOLOG) (HD PROTEIN).
         Mw     Start  End    Seq
        *1400.6 2899   2911   VDGEALVKLSVDR
        *2031.3 645    663    LLSASFLLTGQKNGLTPDR
        *3085.6 1573   1597   LVQYHQVLEMFILVLQQCHKENEDK
         No Match      1086.2 2424.7 2930.3 5423.0 6082.8

   The emowse search program outputs a listing file containing the
   following information.

  Specified search parameters

   Includes all specified parameters such as digest reagent, specified
   error tolerance, specified intact protein Mw and Mw filter percentage.
   All supplied peptide Mws are listed in descending order, followed by
   the total number of entries scanned during the search.

  Short 'hit' listing

   The top 50 scoring proteins are then listed in descending order,
   details include the sequence ID name and brief text identifiers.
   Details are limited to the top 50 scores as a deliberate compromise to
   keep the result listings as short as possible.

  Detailed 'hit' listing

   The top 50 entries are then listed in more detail.The first line
   includes the sequence ID name, the emowse search score (typically a
   few powers of 10), the 'hit' protein Mw and finally an 'accuracy'
   ratio calculated by dividing 'hits' by the total number of peptides
   used for the search. This cannot be used to ascribe significance, but
   experience has shown that anything below 0.3 is generally not worth
   pursuing. Line 2 is the protein text identifier. Subsequent lines list
   'hit' and 'miss' peptides, with the appropriate start, end and
   corresponding sequences of correct peptide matches. 'miss' peptides
   are indicated by 'No match' at the start of the last line for that
   protein.

   Matching peptides marked with a '*' denote partially-cleaved
   fragments.

Data files

   emowse reads in the pre-computed "Frequencies" data file 'Efreqs.dat',
   (See the section "emowse Scoring scheme", above for a description of
   the frequency scores.)

   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

   None.

References

   The paper describing the original 'MOWSE' program is:
    1. D.J.C. Pappin, P. Hojrup and A.J. Bleasby 'Rapid Identification of
       Proteins by Peptide-Mass Fingerprinting'. Current Biology (1993),
       vol 3, 327-332.
       Other references:
    2. Barber M, Bordoli RS, Sedgwick RD, Tyler AN: Fast atom bombardment
       of solids: a new ion source for mass spectrometry. J Chem Soc Chem
       Commun 1981, 7: 325-327.
    3. Dole M, Mack LL, Hines RL, Mobley RC, Ferguson LD, Alice MB:
       Molecular beams of macroions. J Chem Phys 1968, 49:2240-2249.
    4. Meng CK, Mann M, Fenn JB: Of protons or proteins. Z Phys D 1988,
       10: 361-368.
    5. Karas M, Hillenkamp F: Laser desorption ionisation of proteins
       with molecular masses exceeding 10,000 Daltons. Analytical
       Chemistry 1988, 60:2299-2301.
    6. Morris H, Panico M, Taylor GW: FAB-mapping of recombinant-DNA
       protein products. Biochem Biophys Res Commun 1983, 117:299-305.
    7. Morris H, Greer FM: Mass spectrometry of natural and recombinant
       proteins and glycoproteins. Trends in Biotechnology 1988,
       6:140-147.
    8. Weissenbach J, Gyapay G, Dib C, Vignal J, Morissette J, Millasseau
       P, Vaysseix G, Lathrop M: A second generation linkage map of the
       human genome. Nature 1992, 359:794-801.
    9. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH,
       Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie
       WR, Venter JC: Complementary DNA sequencing: expressed sequence
       tags and human genome project. Science 1991, 252:1651-1656.
   10. Lehrach H, Drmanac R, Hoheisel J, Larin Z, Lennon G, Monaco AP,
       Nizetic D, Zehetner G, Poustka A: Hybridization fingerprinting in
       genome mapping and sequencing. In Genome Analysis Volume 1:
       Genetic and Physical Mapping. Cold Spring Harbor Laboratory Press;
       1990:39-81 .
   11. Akrigg D, Bleasby AJ, Dix NIM, Findlay JBC, North ACT, Parry-
       Smith D, Wootton JC, Blundell TI, Gardner SP, Hayes F, Sternberg
       MJE, Thornton JM, Tickle IJ, Murray-Rust P: A protein
       sequence/structure database. Nature 1988, 335:745-746.
   12. Bleasby AJ, Wootton JC: Construction of validated, non- redundant
       composite protein databases. Protein Engineering 1990, 3:153-159.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                         Description
   backtranambig Back translate a protein sequence to ambiguous codons
   backtranseq   Back translate a protein sequence
   charge        Protein charge plot
   checktrans    Reports STOP codons and ORF statistics of a protein
   compseq       Count composition of dimer/trimer/etc words in a sequence
   freak         Residue/base frequency table or plot
   iep           Calculates the isoelectric point of a protein
   mwcontam      Shows molwts that match across a set of files
   mwfilter      Filter noisy molwts from mass spec output
   octanol       Displays protein hydropathy
   pepinfo       Plots simple amino acid properties in parallel
   pepstats      Protein statistics
   pepwindow     Displays protein hydropathy
   pepwindowall  Displays protein hydropathy of a set of sequences

Author(s)

   Alan Bleasby (ajb