NAME

     psiblast - Position-Specific Iterated BLAST, or PSI-BLAST

SYNOPSIS

     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., regu-
          lar 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.  The checkpoint files are  stored  in  a  byte-encoded
     (not human readable) format, so as to prevent roundoff error
     between writing and reading the checkpoint.  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 algo-
     rithms  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  fol-
     lowing   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 Sci-
     ence:

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

     seq1
     ----
     > 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