Provided by: pftools_3.2.12-1_amd64 bug


       xpsa - extended psa header


       xpsa is an extension of the psa(5) file format used by the pftools package to describe and
       store biological sequences.

       xpsa uses keyword=value pairs in the header to include information about the  sequence  or
       the alignment between the sequence and a PROSITE profile (or any other kind of motif). The
       syntax is therefore easily extensible. In this man-page, we focus on the keywords  defined
       and used by the pftools package.

       In  the  following  text  we  will  use  the  more  general  term 'motif' when in fact our
       discussion refers specifically to PROSITE profiles.   Nevertheless  the  keywords  defined
       here can be used by any kind of sequence analysis tool to store and transfer information.

       None  of  the  defined keywords are mandatory and analysis tools have often a length limit
       imposed on the header line. In order to keep the header line  reasonably  short  and  user
       readable,  these  tools  can  easily  remove  individual keyword=value pairs which are not
       important to the specific task at hand.


       The general syntax of the xpsa header is given below. For examples  please  refer  to  the
       corresponding examples section.

       The biological sequence itself starts on the next line following the header and may extend
       over several lines.  If several sequences are contained in the same  file,  each  must  be
       preceded by a header line.

       Syntax of the header line:

              >seq_id/seq_pos { [ keyword=value | free_text ] }

       The header must start with a '>' followed by the fields detailed below:

              seq_id typically  the  accession number and identifier  of the sequence.  This text
                     field should not contain any spaces.

              Note:  If the input sequences have a well defined accession number  and  identifier
                     (as  is the case with SWISS-PROT entries) pfsearch(1) and pfscan(1) will use
                     as seq_id the accession number separated by a '|' from the identifier.
                     If the input sequences are in FASTA format, no guess can be made  about  the
                     accession number or the identifier. Therefore pfsearch(1) and pfscan(1) will
                     use as seq_id  all  text  following  the  '>'  character  up  to  the  first

                     this  field  describes  the  sequence coordinates where a motif matches. The
                     positions are generally given as start_pos-end_pos pairs.
                     If present, this field is separated from the seq_id by a '/' character.

                     is an optional list of defined keyword=value  pairs.  Each  pair  should  be
                     separated from the next or from free text by whitespaces.
                     The  keyword  is case sensitive in the current implementation of the pftools
                     package. It should not exceed 24 characters in length.
                     The value can be numeric  or  alphanumeric.  Values  containing  whitespaces
                     should  be  enclosed  in either single quotes or double quotes.  If the same
                     type of quote appears inside the value it must  be  escaped  using  the  '\'

                     Note:  the pftools do not currently produce quote enclosed values.

                     typically  this  is a description of the sequence. It should not contain any
                     of the defined keyword=value pairs.

       Keywords used by the pfsearch(1) and pfscan(1) programs:

              level  the highest cut-off level (as a value) exceeded by the alignment.
                     The characters 'NA' indicate that the alignment score does not exceed any of
                     the cut-off levels defined in the motif.

                     the highest cut-off level (as a character string) exceeded by the alignment.
                     The characters 'NA' indicate that the alignment score does not exceed any of
                     the cut-off levels defined in the motif.

                     Note:  pfsearch(1) and pfscan(1) only report the first 2 characters  of  the
                            level text string.

                     if  the  motif matches several times on the same sequence, each alignment is
                     numbered incrementally.
                     If the motif is circular, each single repeat is numbered incrementally  with
                     the key repeat_nb (see below).

                     for each single match of a circular motif, this key references the number of
                     the parental total match of the circular motif.

                     Note:  if  a  circular  motif  matches  only  once  on  a  given   sequence,
                            pfsearch(1) and pfscan(1) do not report this key.

                     identifies  the type of match. Either region for a complete match of a motif
                     to a sequence, or repeat for a single repeat of a circular motif.

              motif  the name and/or identifier of the motif.

                     the motif position where the alignment begins.

                     negative offset from the end of the alignment to the end of the motif.

                     the normalized score of the alignment.

                     the raw score of the alignment.

                     if the motif is circular, each individual repeat is  numbered  incrementally
                     with this keyword.

                     negative offset from the end of the alignment to the end of the sequence.
                     In  combination  with the information given by seq_pos this allows to deduce
                     the length of the query sequence.

              strand the sequence strand on which the motif matches, when the search includes the
                     reverse complement of a DNA sequence.  The value is either s for the sens or
                     r for the reverse strand.

       Keywords used by the pfmake(1) and pfw(1) programs:

              weight the weight of a given sequence in a multiple alignment.


       (1)    >O00628|PEX7/73-315      motif=PS50294|WD_REP       raw_score=1336       match_nb=1
              match_type=region seq_end=-491
              >O00628|PEX7/540-801       motif=PS50294|WD_REP      raw_score=1378      match_nb=2
              match_type=region seq_end=-5

              The 2 headers above describe 2 matches  of  the  motif  called  'WD_REP'  onto  the
              sequence  'PEX7'.   Each of the matches onto this single sequence is numbered using
              the the match_nb keyword.  These matches are not individual repeats of  a  circular
              motif as can be seen with the region value of the match_type keyword.
              The  first  match  starts  at position 73 of the sequence and ends at position 315.
              This position is 491 residues away from the end of the input sequence (seq_end).
              The next line following the xpsa(5) header line is the sequence of  the  match  (it
              has been truncated here to help readability).
              The  second  match begins at position 540 of the sequence and terminates 5 residues
              before the end of the input sequence, that is at position 801.

       (2)    >O00628|PEX7/540-582    motif=PS50294|WD_REP     norm_score=7.437     raw_score=180
              match_parent=2  repeat_nb=1  match_type=repeat  level=-1 seq_end=-224 motif_start=1

              This example illustrates the kind of header obtained when aligning a circular motif
              to  a  sequence.  Each  match of this motif (which we will call total match) can be
              composed of several individual repeats of the motif.  Tools  like  pfsearch(1)  and
              pfscan(1)  can  output  each total match followed by all its individual repeats. In
              this example we only show one of the indiviual repeats that  is  part  of  a  total
              match between a circular profile and a sequence.
              The  xpsa(5)  header  above describes a single repeat of a match between a circular
              motif called 'WD_REP' and the sequence 'PEX7'.
              This is the first individual repeat of a match of the circular motif, as identified
              by the repeat_nb keyword. The other individual repeats have not been listed in this
              The total circular motif has at least 2 distinct matches on  the  'PEX7'  sequence,
              because  this  single  repeat  is  part  of  the  second  match as described by the
              match_parent keyword. The parental matches have been  omitted  from  this  example,
              they would be numbered using the match_nb keyword.
              The  normalized  score  of  this  motif  exceeds the cut-off level number -1 (level
              keyword) which is specified in the motif.
              This match starts at position 1 of the profile (motif_start) and  position  540  of
              the  sequence,  it  ends at the end of the motif (motif_end=-1) and position 582 of
              the sequence.
              The next line following the xpsa(5) header line is the sequence of  the  match  (it
              has been truncated here to help readability).


       psa(5), pfsearch(1), pfscan(1), pfw(1), pfmake(1), psa2msa(1)


       This manual page was originally written by Volker Flegel.
       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <>.