/usr/share/doc/blast2/blastpgp.html

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Blastpgp
--------

Blastpgp performs gapped blastp searches and can be used to perform
iterative searches in psi-blast and phi-blast mode. See the PSI-Blast and
PHI-BLAST sections (below) for a description of this binary. The options may be
obtained by executing 'blastpgp -'.

  -T  Produce HTML output [T/F]
    default = F

  -Q  Output File for PSI-BLAST Matrix in ASCII [File Out]  Optional


PSI-Blast
---------

The blastpgp program can do an iterative search in which
sequences found in one round of searching are used to build
a score model for the next round of searching. In this usage,
the program is called Position-Specific Iterated BLAST, or PSI-BLAST.
As explained in the accompanying paper, the BLAST algorithm is
not tied to a specific score matrix. Traditionally, it has been
implemented using an AxA substitution matrix where A is the alphabet size.
PSI-BLAST instead uses a QxA matrix, where Q is the length of the query
sequence; at each position the cost of a letter depends on the position
w.r.t. the query and the letter in the subject sequence.

The position-specific matrix for round i+1 is built from a constrained
multiple alignment among the query and the sequences found with
sufficiently low e-value in round i.  The top part of the output for
each round distinguishes the sequences into: sequences found
previously and used in the score model, and sequences not used in the
score model. The output currently includes lots of diagnostics
requested by users at NCBI. To skip quickly from the output of
one round to the next, search for the string "producing", which is
part of the header for each round and likely does not appear elsewhere
in the output. PSI-BLAST "converges" and stops if all sequences
found at round i+1 below the e-value threshold were already in
the model at the beginning of the round.

There are several blastpgp parameters specifically for PSI-BLAST:
-j   is the maximum number of rounds (default 1; i.e., regular BLAST)
-h   is the e-value threshold for including sequences in the
     score matrix model (default 0.001)
-c   is the "constant" used in the pseudocount formula specified in the
     paper (default 10)

The -C and -R flags provide a "checkpointing" facility whereby
a score model can be stored and later reused.
   -C  stores the query and frequency count ratio matrix in a
                  file
   -R  restarts from a file stored previously.
When using -R, it is required that the query specified on the command line
match exactly the query in the restart file.

Two additional arguments specify the format of the input/output
checkpoint file
   -q  Format of the input checkpoint file:
        0: the default: a byte-encoded (not human readable) format
        1: a text ASN.1 scoremat object
        2: a binary ASN.1 scoremat object
   -u  Format of the output checkpoint file:
        0: the default: a byte-encoded (not human readable) format
        1: a text ASN.1 scoremat object
        2: a binary ASN.1 scoremat object

Users who also develop their own sequence analysis software may wish
to develop their own scoring systems. For this purpose the code
in posit.c that writes out the checkpoint can be easily adapated to
write out scoring systems derived by other algorithms in such
a way that PSI-BLAST can read the files in later.
The checkpoint structure is general in the sense that it can handle
any position-specific matrix that fits in the Karlin-Altschul
statistical framework for BLAST scoring.

The -B flag provides a way to jump start PSI-BLAST from a master-slave
multiple alignment computed outside PSI-BLAST.  The multiple alignment
must include the query sequence as one of the sequences, but it need
not be the first sequence.  The multiple alignment must be specified
in a format that is derived from Clustal, but without some headers and
trailers.  See example below. The rules are also described by the
following words.  Suppose the multiple alignments has N sequences.  It
may be presented in 1 or more blocks, where each block presents a
range of columns from the multiple alignment.  E.g., the first block
might have columns 1-60, the second block might have columns 61-95,
the third block might have columns 96-128. Each block should have N
rows, 1 row per sequence.  The sequences should be in the same order
in every block.  Blocks are separated by 1 or more blank lines.
Within a block there are no blank lines, and each line consists of 1
sequence identifier followed by some white space followed by
characters (and gaps) for that sequence in the multiple alignment.  In
each column, all letters must be in upper case, or all letters must be
in lower case.  Upper case means that this column is to be given
position-specific scores. Lower-case means to use the underlying
matrix (specified by -M) for this column; e.g., if the query sequence
has an 'l' residue in the column, then the standard scores for
matching an L are used in the column.

A sample usage would be:

  blastpgp -i seq1 -B align1 -j 2 -d nr

where seq1 is the query
      align1 is the alignment file
      -j 2 indicates to do 2 rounds
      -d nr indicates to use the nr database

The example files
    seq1
    align1
copied below were kindly supplied by L. Aravind from a paper
he and Chris Ponting published in Protein Science:

Aravind L, Ponting CP, Homologues of 26S proteasome subunits 
are regulators of transcription and translation, Protein Science 
7(1998) 1250-1254.

L. Aravind (aravind@ncbi.nlm.nih.gov) was the first user
and helped define how -B should work. Y. Wolf (wolf@ncbi.nlm.nih.gov)
helped design a more flexible input format for the alignments.
If you like how -B works, let them know.
If you do not like how -B works, complain to 
A. Schaffer(schaffer@helix.nih.gov) who did the implementation.

seq1
----
&gt; 26SPS9_Hs 
IHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEA
LKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKL
SKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPP


align1
------
26SPS9_Hs     IHAAEEKDWKTAYSYFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgklalryagrqtealkcvaqasknr
F57B9_Ce      LHAADEKDFKTAFSYFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsaklalkyngsdldamkaiaaaaqk
YDL097c_Sc    ILHCEDKDYKTAFSYFFESFESYhnltthnsyekacqvlkymllskimlnliddvknilnakytketyqsrgidamkavae
YMJ5_Ce       LYSAEERDYKTSFSYFYEAFEGFasigdkinatsalkymilckimlneteqlagllaakeivayqkspriiairsmadafr
FUS6_ARATH    KNYIRTRDYCTTTKHIIHMCMNAilvsiemgqfthvtsyvnkaeqnpetlepmvnaklrcasglahlelkkyklaarkfld
COS41.8_Ci    SLDYKLKTYLTIARLYLEDEDPVqaemyinrasllqnetadeqlqihykvcyarvldyrrkfleaaqrynelsyksaihet
644879        KCYSRARDYCTSAKHVINMCLNVikvsvylqnwshvlsyvskaestpeiaeqrgerdsqtqailtklkcaaglaelaarky
YPR108w_Sc    IHCLAVRNFKEAAKLLVDSLATFtsieltsyesiatyasvtglftlertdlkskvidspellslisttaalqsissltisl
eif-3p110_Hs  SKAMKMGDWKTCHSFIINEKMNGkvw-------------------------------------------------------
T23D8.4_Ce    SKAMLNGDWKKCQDYIVNDKMNQkvw-------------------------------------------------------
YD95_Sp       IYLMSIRNFSGAADLLLDCMSTFsstellpyydvvryavisgaisldrvdvktkivdspevlavlpqnesmssleacinsl
KIAA0107_Hs   LYCVAIRDFKQAAELFLDTVSTFtsyelmdyktfvtytvyvsmialerpdlrekvikgaeilevlhslpavrqylfslyec
F49C12.8_Hs   LYRMSVRDFAGAADLFLEAVPTFgsyelmtyenlilytvitttfaldrpdlrtkvircnevqeqltggglngtlipvreyl
Int-6_Mm      KFQYECGNYSGAAEYLYFFRVLVpatdrnalsslwgklaseilmqnwdaamedltrlketidnnsvssplqslqqrtwlih

26SPS9_Hs     sladfekaltdy-----------------------------------------------------------------------------------
F57B9_Ce      rslkdfqvafgsf----------------------------------------------------------------------------------
YDL097c_Sc    aynnrslldfntalkqy------------------------------------------------------------------------------
YMJ5_Ce       krslkdfvkalaeh---------------------------------------------------------------------------------
FUS6_ARATH    vnpelgnsyneviapqdiatygglcalasfdrselkqkvidninfrnflelvpdvrelindfyssryascleylasl------------------
COS41.8_Ci    eqtkalekalncailapagqqrsrmlatlfkdercqllpsfgilekmfldriiksdemeefar--------------------------------
644879        kqaakclllasfdhcdfpellspsnvaiygglcalatfdrqelqrnvissssfklflelepqvrdiifkfyeskyasclkmldem----------
YPR108w_Sc    yasdyasyfpyllety-------------------------------------------------------------------------------
eif-3p110_Hs  -----------------------------------------------------------------------------------------------
T23D8.4_Ce    -----------------------------------------------------------------------------------------------
YD95_Sp       ylcdysgffrtladve-------------------------------------------------------------------------------
KIAA0107_Hs   rysvffqslavv-----------------------------------------------------------------------------------
F49C12.8_Hs   esyydchydrffiqlaale----------------------------------------------------------------------------
Int-6_Mm      wslfvffnhpkgrdniidlflyqpqylnaiqtmcphilrylttavitnkdvrkrrqvlkdlvkviqqesytykdpitefveclyvnfdfdgaqkk

26SPS9_Hs     ----RAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPP
F57B9_Ce      ----PQELQMDPVVRKHFHSLSERMLEKDLCRIIEPYSFVQIEHVAQQIGIDRSKVEKKLSQMILDQKLSGSLDQGEGMLIVFEIAV
YDL097c_Sc    ----EKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLDTQQVEGKLSQMILDKIFYGVLDQGNGWLYVYETPN
YMJ5_Ce       ----KIELVEDKVVAVHSQNLERNMLEKEISRVIEPYSEIELSYIARVIGMTVPPVERAIARMILDKKLMGSIDQHGDTVVVYPKAD
FUS6_ARATH    ----KSNLLLDIHLHDHVDTLYDQIRKKALIQYTLPFVSVDLSRMADAFKTSVSGLEKELEALITDNQIQARIDSHNKILYARHADQ
COS41.8_Ci    ----QLMPHQKAITADGSNILHRAVTEHNLLSASKLYNNIRFTELGALLEIPHQMAEKVASQMICESRMKGHIDQIDGIVFFERRET
644879        ----KDNLLLDMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSHSKILYARDVDQ
YPR108w_Sc    ----ANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRPDN
eif-3p110_Hs  ----DLFPEADKVRTMLVRKIQEESLRTYLFTYSSVYDSISMETLSDMFELDLPTVHSIISKMIINEELMASLDQPTQTVVMHRTEP
T23D8.4_Ce    ----NLFHNAETVKGMVVRRIQEESLRTYLLTYSTVYATVSLKKLADLFELSKKDVHSIISKMIIQEELSATLDEPTDCLIMHRVEP
YD95_Sp       ----VNHLKCDQFLVAHYRYYVREMRRRAYAQLLESYRALSIDSMAASFGVSVDYIDRDLASFIPDNKLNCVIDRVNGVVFTNRPDE
KIAA0107_Hs   ----EQEMKKDWLFAPHYRYYVREMRIHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPDS
F49C12.8_Hs   ----SERFKFDRYLSPHFNYYSRGMRHRAYEQFLTPYKTVRIDMMAKDFGVSRAFIDRELHRLIATGQLQCRIDAVNGVIEVNHRDS
Int-6_Mm      lrecESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISINMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAV





PHI-Blast
---------

PHI-BLAST (Pattern-Hit Initiated BLAST) is a search
program that combines matching of regular expressions
with local alignments surrounding the match.
The most important features of the program have been
incorporated into the BLAST software framework
partly for user convenience and partly so that
PHI-BLAST may be combined seamlessly with PSI-BLAST.
Other features that do not fit into the BLAST framework
will be released later as a separate program and/or
separate Web page query options.

One very restrictive way to identify protein motifs
is by regular expressions that must contain each instance
of the motif. The PROSITE database is a compilation of
restricted regular expressions that describe protein motifs.
Given a protein sequence S and a regular expression pattern P
occurring in S, PHI-BLAST helps answer the question:
What other protein sequences both contain an occurrence of P
and are homologous to S in the vicinity of the pattern occurrences?
PHI-BLAST may be preferable to just searching for pattern occurrences
because it filters out those cases where the pattern occurrence is
probably random and not indicative of homology.
PHI-BLAST may be preferable to other flavors of BLAST because
it is faster and because it allows the user to express
a rigid pattern occurrence requirement.

The pattern search methods in PHI-BLAST are based on the
algorithms in:

R. Baeza-Yates and G. Gonnet, Communications of the ACM 35(1992), pp. 74-82.
S. Wu and U. Manber, Communications of the ACM 35(1992), pp. 83-91.

The calculation of local alignments is done using a method
very similar to (and much of the same code as) gapped BLAST.
However, the method of evaluating statistical significance is different, and
is described below.

In the stand-alone mode the typical PHI-BLAST usage looks like:
  blastpgp -i  -k  -p patseedp

  where -i is followed by the file containing the query in FASTA format
  where -k is followed by the file containing the pattern in a syntax given below
  and "patseedp" indicates the mode of usage,  not representing any file.

The syntax for the query sequence is FASTA format as for all other
BLAST queries. The syntax for patterns follows the rules of
PROSITE and is documented in detail below.
The specified pattern is not required to be in the PROSITE list.
Most of the other BLAST flags can be used with PHI-BLAST.
One important exception is that PHI-BLAST requires gapped
alignments (i.e. forbids -g F in the flags) because ungapped
alignments do not make sense for almost all patterns in PROSITE.

There is a second mode of PHI-BLAST usage that is important when
the specified pattern occurs more than 1 time in the query.
In this case, the user may be interested in restricting the
search for local alignments to a subset of the pattern occurrences.
This can be done with a search that looks like:
   blastpgp -i  -k  -p seedp

in which case the use of the "seedp" option requires the user to
specify the location(s) of the interesting pattern occurrence(s)
in the pattern file. The syntax for how to specify pattern
occurrences is below. When there are multiple pattern occurrences in the
query it may be important to decide how many are of interest because
the E-value for matches is effectively multiplied by the number
of interesting pattern occurrences.

The PHI-BLAST Web page supports only the "patseedp" option.

PHI-BLAST is integrated with PSI-BLAST. In the command-line
mode, PSI-BLAST can be invoked by using the -j option, as usual.
When this is done as:
   blastpgp -i  -k  -p patseedp -j

then the first round of searching uses PHI-BLAST and all subsequent
rounds use PSI-BLAST.
In the Web page setting, the user must explicitly invoke one round
at a time, and the PHI-BLAST Web page provides the option to
initiate a PSI-BLAST round with the PHI-BLAST results.
To describe a combined usage, use the term "PHI-PSI-BLAST"
(Pattern-Hit Initiated, Position-Specific Iterated BLAST).

Determining statistical significance.

When a query sequence Q matches a database sequence D in PHI-BLAST,
it is useful to subdivide Q and D into 3 disjoint pieces
    Qleft Qpattern Qright
    Dleft Dpattern Dright

The substrings Qpattern and Dpattern contain the pattern specified
in the pattern file. The pieces Qpattern and Dpattern are aligned
and that alignment is displayed as part of the PHI-BLAST output,
but the score for that alignment is mostly ignored.
The "reduced" score r of an alignment is the sum of the scores obtained
by aligning  Qleft with Dleft and by aligning Qright with Dright.

The expected number of alignments with a reduced score &gt;= x
is given by:
       CN(Lambda*x + 1)e^(-Lambda *x)
where:

C and Lambda are "constants" depending on the score matrix and the
gap costs.
N is (number of occurrences of pattern in database) * (number of
      occurrences of pattern in Q)
e is the base of the natural logarithm.

It is important to understand that this method of computing
the statistical significance of a PHI-BLAST alignment is mathematically
different from the method used for BLAST and PSI-BLAST alignments.
However, both methods provide E-values, so they the E_values are
displayed with a similar output syntax.

Rules for pattern syntax for PHI-BLAST.

The syntax for patterns in PHI-BLAST follows the conventions
of PROSITE. When using the stand-alone program, it
is permissible to have multiple patterns in a file separated
by a blank line between patterns. When using the Web-page
only one pattern is allowed per query.

Valid protein characters for PHI-BLAST patterns:
    ABCDEFGHIKLMNPQRSTVWXYZU

Valid DNA characters for PHI-BLAST patterns:
    ACGT

Other useful delimiters:
    [ ]    means any one of the characters enclosed in the brackets
        e.g., [LFYT] means one occurrence of L or F or Y or T
    -      means nothing (this is a spacer character used by PROSITE)
    x with nothing following means any residue
    x(5)  means 5 positions in which any residue is allowed (and similarly for any other
          single number in parentheses after x)
    x(2,4) means 2 to 4 positions where any residue is allowed,
           and similarly for any other two numbers separated by a comma;
           the first number should be &lt; the second number.
    &gt;      can occur only at the end of a pattern and means nothing
           it may occur before a period
           (another spacer used by PROSITE)

    .      may be used at the end of the pattern and means nothing

When using the stand-alone program, the pattern should
be in a file, with the first line starting:
 ID
followed by 2 spaces and a text string giving the pattern a name.

There should also be a line starting
 PA
followed by 2 spaces followed by the pattern description.

All other PROSITE codes in the first two columns are allowed,
but only the HI code, described below is relevant to PHI-BLAST.

Here is an example from PROSITE.

ID   CNMP_BINDING_2; PATTERN.
AC   PS00889;
DT   OCT-1993 (CREATED); OCT-1993 (DATA UPDATE); NOV-1995 (INFO UPDATE).
DE   Cyclic nucleotide-binding domain signature 2.
PA   [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
NR   /RELEASE=32,49340;
NR   /TOTAL=57(36); /POSITIVE=57(36); /UNKNOWN=0(0); /FALSE_POS=0(0);
NR   /FALSE_NEG=1; /PARTIAL=1;
CC   /TAXO-RANGE=??EP?; /MAX-REPEAT=2;

The line starting
    ID
gives the pattern a name.
The lines starting
     AC, DT, DE, NR, NR, CC
are relevant to PROSITE users, but irrelevant to PHI-BLAST.
These lines are tolerated, but ignored by PHI-BLAST.

The line starting
     PA
describes the pattern as:
      one of LIVMF
followed by
      G
followed by
      E
followed by
      any single character
followed by
      one of GAS
followed by
      one of LIVM
followed by
      any 5 to 11 characters
followed by
      R
followed by
      one of STAQ
followed by
      A
followed by
      any single character
followed by
      one of LIVMA
followed by
      any single character
followed by
      one of STACV

In this case the pattern ends with a period.
It can end with nothing after the last specifying symbol
or any number of &gt; signs or periods or combination thereof.

Here is another example, illustrating the use of an HI line.

ID    ER_TARGET; PATTERN.
PA  [KRHQSA]-[DENQ]-E-L&gt;.
HI (19 22)
HI (201 204)

In this example, the HI lines specify that the pattern
occurs twice, once from positions 19 through 22 in the
sequence and once from positions 201 through 204 in the
sequence.
These specifications are relevant when stand-alone PHI-BLAST is
used with the
     seedp
option, in which the interesting occurrences of the pattern
in the sequence are specified. In this case the
HI lines specify which occurrence(s) of the pattern
should be used to find good alignments.

In general, the seedp option is more useful than the
standard patternp option ONLY when the
pattern occurs K &gt; 1 times in the sequence AND
the user is interested in matching to J &lt; K of those
occurrences.
Then using the HI lines enables the user to specify which
occurrences are of interest.

Additional functionality related to PHI-BLAST.

PHI-BLAST takes as input both a sequence and a query containing
that sequence and searches a sequence database for
other sequences containing the same pattern and having a good alignment.
One may be interested in asking two related, simpler questions:

1. Given a sequence and a database of patterns, which patterns occur
in the sequence and where?

2. Given a pattern and a sequence database, which sequences contain the
pattern and where?

These queries can be answered wih software closely related to PHI-BLAST,
but they do not fit into the output framework of BLAST because the
answers are simple lists without alignments and with no notion of
statistical significance.

The NCBI toolbox includes another program, currently called
     seedtop
to answer the two queries above.

Query 1 can be asked with:
  seedtop -i  -k  -p patmatchp

Query 2 can be asked with:
  seedtop -d  -k  -p patternp

The -k argument is used similarly in all queries and the file
format is always the same. The standard pattern database is
PROSITE, but others (or a subset) can be used.
There are plans afoot to offer the patmatchp query (number 1) on
the PHI-BLAST web page or in its vicinity, but this would
be restricted to having PROSITE as the pattern database.

   Documentation for PSI-TBLASTN

PSI-BLASTN is a variant of blastall that searches a protein query
sequence against a nucleotide sequence database using a position
specific matrix created by PSI-BLAST. The nucleotide sequence database
is dynamically translated in all reading frames during PSI-TBLASTN
search. Using a position specific matrix may enable finding more
distantly related sequences.

Programs: 
blastpgp        [takes a protein query and perform PSI-BLAST search to 
                creates a position specific matrix using a protein 
                database]

blastall        [reads position specific matrix and performs PSI-TBLASTN 
                search]

Usage:
A user would typically run blastpgp to create and save a position
specific matrix, followed by a run of blastall for PSI-TBLASTN search.

blastpgp must be executed with -C option followed by a file name to
save position specific score matrix.

blastall with "-p psitblastn" option executes PSI-TBLASTSN search, and
-R option followed by a file name specifying the file that contains
position specific score matrix. All other options that apply when
using "blastall -p tblastn ..." also apply when using "blastall -p
psitblastn ...", but there are some restrictions to parameters: 1) The
query must be the same as the one used in blastpgp for creating a
position specific matrix. 2) By default, blastpgp has filtering off
(-F F) and blastall has filtering on (-F T). To ensure consistent
usage of the blastpgp/psitblastn combination, the -F option should be
explicitly set in one or the other run.


Example: 
One may run PSI-BLST to create and save a position specific score matrix
as follows: 

        blastpgp -d nr -i ff.chd -j 2 -C ff.chd.ckp

Position specific score matrix is saved in ff.chd.ckp. Then, using 
this matrix, one may run PSI-TBLASTN search:

        blastall -i ff.chd -d yeast -p psitblastn -R ff.chd.ckp

Note that this allows the score matrix to be constructed using one
database (nr in the example) and then used to search a second database
(yeast in the example). Even if the two database names are the same,
blastpgp uses the protein version while "blastall -p psitblastn" uses
the DNA version.
</pre>
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blast2 1:2.2.26.20120620-8 / usr / share / doc / blast2 / blastpgp.html
