epestfind.txt

emboss的linux版本的源代码

                                 epestfind 



Function

   Finds PEST motifs as potential proteolytic cleavage sites

Description

   epestfind allows rapid and objective identification of PEST motifs in
   protein target sequences. Briefly, the PEST hypothesis was based on a
   literature survey that combined both information on protein stability
   as well as protein primary sequence information. Initially, the study
   relied on 12 short-lived proteins with well-known properties [1], but
   was continually extended later [2,3]. The initial group of proteins
   included E1A, c-myc, p53, c-fos, v-myb, P730 phytochrome, heat shock
   protein 70 (HSP 70), HMG-CoA reductase, tyrosine aminotransferase
   (TAT), ornithine decarboxylase (ODC), alpha-Casein and beta-Casein.
   Although all these proteins exerted various different cellular
   functions it became apparent that they shared high local
   concentrations of amino acids proline (P), glutamic acid (E), serine
   (S), threonine (T) and to a lesser extent aspartic acid (D). From that
   it was concluded that PEST motifs reduce the half-lives of proteins
   dramatically and hence, that they target proteins for proteolytic
   degradation.

   PEST means Black Death in German, so that the name of this programme
   sounds a bit strange, at least in our ears.

Algorithm

   PEST motifs were defined as hydrophilic stretches of at least 12 amino
   acids length with a high local concentration of critical amino acids.
   Remarkably, negatively charged amino acids are clustered within these
   motifs while positively charged amino acids, arginine (R), histidine
   (H) and lysine (K) are generally forbidden.

   The epestfind algorithm defines the last criterion even more
   stringently in that PEST motifs are required to be flanked by
   positively charged amino acids. Though this implication greatly
   facilitates computer scanning, a few PEST sequences might be missed.
   Especially sequences with a high local concentration of critical amino
   acids but with a long distance between positively charged amino acids
   are error prone. Due to their length, these PEST motifs might become
   diluted, which results in scores apparently lower than initially
   expected. Another side effect of scanning for positively charged amino
   acids is that very long PEST motifs are sub-divided into adjacent
   smaller ones. However, identification of PEST motifs is achieved by an
   initial scan for positively charged amino acids arginine (R),
   histidine (H) and lysine (K) within the specified protein sequence.
   All amino acids between the positively charged flanks are counted and
   only those motifs are considered further, which contain a number of
   amino acids equal to or higher than the window-size parameter.
   Additionally, all 'valid' PEST regions are required to contain at
   least one proline (P), one aspartate (D) or glutamate (E) and at least
   one serine (S) or threonine(T). Sequences that do not meet the above
   criteria are classified as 'invalid' PEST motifs and excluded from
   further analysis.

   The quality of 'valid' PEST motifs is refined by means of a scoring
   parameter based on the local enrichment of critical amino acids as
   well as the motif's hydrophobicity. Enrichment of D, E, P, S and T is
   expressed in mass percent (w/w) and corrected for one equivalent of D
   or E, one of P and one of S or T. Calculation of hydrophobicity
   follows in principle the method of J. Kyte and R.F. Doolittle [4]. For
   simplified calculations, Kyte-Doolittle hydropathy indices, which
   originally ranged from -4.5 for arginine to +4.5 for isoleucine, were
   converted to positive integers. This was achieved by the following
   linear transformation, which yielded values from 0 for arginine to 90
   for isoleucine.

        Hydropathy index = 10 * Kyte-Doolittle hydropathy index + 45

   The motif's hydrophobicity is calculated as the sum over the products
   of mole percent and hydrophobicity index for each amino acid species.
   The desired PEST score is obtained as combination of local enrichment
   term and hydrophobicity term as expressed by the following equation:

          PEST score = 0.55 * DEPST - 0.5 * hydrophobicity index.

   Although, the formula above differs from the publication [1], it is in
   fact the correct one, which was also implemented in the original BASIC
   programme (personal communication). In addition, the programme
   includes a correction for the hydropathy index of tyrosine, introduced
   by Robert H. Stellwagen from the University of Southern California.
   However, PEST scores can range from -45 for poly-isoleucine to about
   +50 for poly-aspartate plus one proline and one serine. 'Valid' PEST
   motifs below the threshold score (5.0) are considered as 'poor', while
   PEST scores above the threshold score are of real biological interest.
   The higher the PEST score, the more likely is degradation of proteins
   mediated via 'potential' PEST motifs in eukaryotic cells.

   Presently, all modified Kyte-Doolittle hydropathy indices are
   hard-coded into the programme, which might change in future.

   The array of linear transformed Kyte-Doolittle hydropathy indices
   (ltkdhi) is listed in alphabetical order below. (A-M and N-Z as well
   as N-terminus and C-terminus)

   63, 10, 70, 10, 10, 72, 41, 13, 90, 0, 6, 82, 64, 10, 0, 29, 10, 0,
   36, 38, 0, 87, 36, 45, 58, 10, 0, 0

   The linear transformation was ltkdhi = 10 * kdhi + 45
   All values range from Argine R = 0 to Isoleucine I = 90
   B=(N|D)=10 since N=10 and D=10
   Z=(Q|E)=10 since Q=10 and E=10
   X=10*0+45=45

Usage

   Here is a sample session with epestfind


% epestfind -graph cps -invalid 
Finds PEST motifs as potential proteolytic cleavage sites
Input protein sequence: exu2_drops.embl
Window length [10]: 
Sort order of results
      1 : length
      2 : position
      3 : score
Sort order of results [score]: 
Output file [exu2_drops.epestfind]: 

Created epestfind.ps

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Protein sequence USA to be analysed.
   -window             integer    [10] Minimal distance between positively
                                  charged amino acids. (Integer 2 or more)
   -order              selection  [score] Name of the output file which holds
                                  the results of the analysis. Results may be
                                  sorted by length, position and score.
  [-outfile]           outfile    [*.epestfind] Name of file to which results
                                  will be written.
   -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)

   Additional (Optional) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acids properties and
                                  molecular weight data file
   -threshold          float      [+5.0] Threshold value to discriminate weak
                                  from potential PEST motifs. Valid PEST
                                  motifs are discriminated into 'poor' and
                                  'potential' motifs depending on this
                                  threshold score. By default, the default
                                  value is set to +5.0 based on experimental
                                  data. Alterations are not recommended since
                                  significance is a matter of biology, not
                                  mathematics. (Number from -55.00 to 55.00)

   Advanced (Unprompted) qualifiers:
   -[no]potential      boolean    [Y] Decide whether potential PEST motifs
                                  should be printed.
   -[no]poor           boolean    [Y] Decide whether poor PEST motifs should
                                  be printed.
   -invalid            boolean    [N] Decide whether invalid PEST motifs
                                  should be printed.
   -[no]map            boolean    [Y] Decide whether PEST motifs should be
                                  mapped to sequence.

   Associated qualifiers:

   "-sequence" 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

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   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

   epestfind reads any normal protein sequence USA.

  Input files for usage example

  File: exu2_drops.embl

ID   EXU2_DROPS     STANDARD;      PRT;   477 AA.
AC   Q24617;
DT   01-NOV-1997 (Rel. 35, Created)
DT   01-NOV-1997 (Rel. 35, Last sequence update)
DT   01-NOV-1997 (Rel. 35, Last annotation update)
DE   Maternal exuperantia 2 protein.
GN   EXU2.
OS   Drosophila pseudoobscura (Fruit fly).
OC   Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
OC   Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila.
OX   NCBI_TaxID=7237;
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=94350208; PubMed=8070663;
RA   Luk S.K.-S., Kilpatrick M., Kerr K., Macdonald P.M.;
RT   "Components acting in localization of bicoid mRNA are conserved among
RT   Drosophila species.";
RL   Genetics 137:521-530(1994).
CC   -!- FUNCTION: ENSURES THE PROPER LOCALIZATION OF THE MRNA OF THE
CC       BICOID GENE TO THE ANTERIOR REGIONS OF THE OOCYTE THUS PLAYING
CC       A FUNDAMENTAL ROLE IN THE ESTABLISHMENT OF THE POLARITY OF THE
CC       OOCYTE. MAY BIND THE BCD MRNA (BY SIMILARITY).
CC   --------------------------------------------------------------------------
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