
                          SEQSEARCH documentation
                                      
   

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Generate database hits (sequences) for nodes in a DCF file (domain
   classification file) by using PSI-BLAST

2.0 INPUTS & OUTPUTS

   SEQSEARCH reads a directory of i. single protein sequences or ii. set
   of protein sequences (aligned or unaligned) and generates a DHF file
   ('domain hits file') of sequence relatives (hits) for each file in the
   input directory. The hits are sequence relatives to the input
   sequences and are found by using PSIBLAST. Only unique hits are
   generated; only one of a set of identical hits returned by PSIBLAST is
   retained.
   Typically, aligned sequences within a DAF file ('domain alignment
   file') are input and the DHF file output is annotated with domain
   classification data.
   PSIBLAST must be installed on the system that is running SEQSEARCH
   (see 'Notes' below). The base name of an input file is used as the
   base name for the corresponding output file. The paths and extensions
   for the sequence files (input) and domain hits files (output) are
   specified by the user. The name of the BLAST-indexed database to
   search are also user-specified. A log file is also written.

3.0 INPUT FILE FORMAT

   The format of the domain alignment file is described in DOMAINALIGN
   documentation.
   If other sequences or sequence sets (aligned or unaligned) are used as
   input, all of the common file formats are supported.

  Input files for usage example

  File: all.scop

ID   D1CS4A_
XX
EN   1CS4
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

  File: swnew

>ODO2_FUGRU Q90512 DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTA
RATE DEHYDROGENASE COMPLEX PRECURSOR (EC 2.3.1.61) (E2) (E2K) (FRAGMENT).
SSVCRRLIFRTSRPGERASSQNSFHVRYFRTSVVHRDDLVTVKTPAFAESVTEGDVRWEK
AVGDSVTEDEVVCEIETDKTSVQVPSPAAGVIEELLVPDGGKVEGGTPLFKLRKGAAAEA
APSSVTEPVTAAPPPPPPPVSAPTAMPSVPPVPTQALQAKPVPAPTLPEPSTLGGRGESR
VKMSRMRLRIAQRLKEAQNTCAMLTTFNEVDMSNIQEMRTLHKDAFLKKHSIKLGFMSAF
VKAAAHALTDQPAVNAVIDGATNEIVYRDYVDISVAVATPKGLVVPVIRNVETMNFADIE
RTINALGEKARNNELAVEDMDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHGIFQRPV
AVDGKAEIRPMMYVALTYDHRLVDGREAVTFLRKIKAAVEDPRALLLDM
>TM21_FUGRU Q90515 TRANSMEMBRANE PROTEIN TMP21 PRECURSOR (S31III125).
MARLTALLFLPVLIESAFSISFFLPVNTRKCLREEIHKDVLVTGEYEISEQVVTVHTSST
VVGDGSIFKITDSSSHTLYSKEDATKGKFAFTTEDYDMFEVCFESKCTGRVPDQLVNLDM
KHGVEAKNYEEIAKVEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRV
LYFSIFSMFCLIGLATWQVFYLRRFFKAKKLIE
>CO9_FUGRU P79755 COMPLEMENT COMPONENT C9 PRECURSOR.
MRTEAALQLGFCALCVMLALLGEGMGRELPDPPAVNCVWSRWAPWSSCDPCTNTRRRSRG
VEVFGQFAGIACQGSVGDREYCITNAKCNLPPPRECSDSEFQCESGSCIKLRLKCNGDYD
CEDGSDEDCEPLRKTCPPTVLDTNEQGRTAGYGINILGADPRMNPFNNDFFNGRCDKVRN
PNTLQLDRLPWNIGVLNYQTLVEETASREIYEDSYSLLREMLKEMSIKVDAGLSFKFKST
EPSMSNNSLKLDASLEYEKKTMIKDVSELTNIKNKSFMRVKGRLQLSTYRMRSHQLQVAD
EFVAHVKSLPLEYEKGIYYAFLEDYGTHYTKNGKSGGEYELVYVLNQDTIKAKNLTERKI
QECLKIGIEAEFATTSVQDGKAHAKLNKCDDVTTKSQGDVEGKAVVDNVMTSVKGGSLES
AVTMRAKLNKEGVMDIATYQNWARTIASAPALINSEPEPIYMLIPTDIPGANSRIANLKQ
ATADYVAEYNVCKCRPCHNGGTLALLDGKCICMCSNLFEGLGCQNFKGDKARVPAARPAV
TQEGNWSCWSSWSNCQGQKRSRTRYCNTEGVLGAECRGEIRSEEYC
>E2BB_FUGRU Q90511 TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GD
P-GTP EXCHANGE FACTOR) (S20I15).
MPGADKEVDLTERIEAFLSDLKRGGSGTGPLRGSSETARETTALLRRITAQARWSSAGDL
MEIIRKEGRRLIAAQPSETTVGNMIRRVLKIIREEYARSRGSSEEADQQESLHKLLTSGG
LSEENFRQHFAALRANVIEAINELLTELEGTTDNIAMQALEHIHSNEVIMTVGRSRTVEA
FLKDAARKRKFHVIVAECAPFCQGHKMATSLSTAGIETTVIADAAIFAVMSRVNKVIIGT
QTVLANGGLRAVNGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDTFHKFVSPHEVLP
FTEGEILSKVNVHCPVFDYVPPELITLFISNIGGHAPSYIYRLMSELYHPEDHEL
>FOS_FUGRU P53450 P55-C-FOS PROTO-ONCOGENE PROTEIN.
MMFTSFNAECDSSSRCSASPVGDNLYYPSPAGSYSSMGSPQSQDFTDLTASSASFIPTVT
AISTSPDLQWMVQPLISSVAPSHRAHPYSPSPSYKRTVMRSAASKAHGKRSRVEQTTPEE
EEKKRIRRERNKQAAAKCRNRRRELTDTLQAETDQLEDEKSSLQNDIANLLKEKERLEFI
LAAHQPICKIPSQMDTDFSVVSMSPVHACLSTTVSTQLQTSIPEATTVTSSHSTFTSTSN
SIFSGSSDSLLSTATVSNSVVKMTDLDSSVLEESLDLLAKTEAETARSVPDVNLSNSLFA
AQDWEPLHATISSSDFEPLCTPVVTCTPACTTLTSSFVFTFPEAETFPTCGVAHRRRSNS
NDQSSDSLSSPTLLAL
>FABP_FUGRU O42494 FATTY ACID BINDING PROTEIN.
MSFSGKYQQVSQENFEPFMKAIGLPDEVIQQVKELKSTSEIEQNGNDFKITITTGPKVTV
NKFTIGKETEMDTITGEKIKTVFHLDGNKLKVSLKGIESVTELADPNTITMTLGDVVYKT
TSKRM
>KPB2_FUGRU Q9W6R1 PHOSPHORYLASE B KINASE ALPHA REGULATORY CHAIN, LIVER ISOFORM
 (PHOSPHORYLASE KINASE ALPHA L SUBUNIT).
MRSRSNSGVRLDGYARLVHETILGFQNPVTGLLPASVQKKDAWVRDNVYSILAVWGLGMA
YRKNADRDEDKAKAYELEQSVVKLMQGLLHCMMRQVAKVEKFKHTQSTTDCLHAKYDTST
CATVVGDDQWGHLQVDATSIYLLMLAQMTASGLRIISNLDEVAFVQNLVFYIEAAYKVAD
YGMWERGDKTNQGLPELNGSSVGMAKAALEAIDELDLFGAHGGPKSVIHVLPDEVEHCQS
ILCSMLPRASPSKEIDAGLLSVISFPAFAVEDADLVTITKSEIINKLQGRYGCCRFIRDG
YHCPKEDPTRLHYDPAELKLFENIECEWPVFWTYLILDGIFAEDQVQVQEYREALEGVLI
RGKNGIKLLPELYTVPFDKVEEEYRNPHSVDREATGQLPHMWEQSLYILGCLLAEGFLAP
GEIDPLNRRFSTSFKPDVVVQVCVLAESQEIKALLSEQGMVVQTVAEVLPIRVMSARVLS
QIYVRLGNCKKLSLSGRPYRHIGVLGTSKFYEIRNHTYTFTPQFLDQHHFYLALDNQMIV
EMLRTELAYLSSCWRMTGRPTLTFPVTRSMLVEDGDAVDPCILSTLRKLQDGYFAGARVQ
MSDLSTFQTTSFHTRLSFLDEEHDDSLLEDDEEQEEEEEDKFEDDYNNYGPSGNNQVCYV
SKDKFDQYLTQLLHSTTQKCHLPPIQRGQHHVFSAEHTTRDILSFMAQVQGLNVPKSSMY
LPVTPLKSKHRRSLNLLDVPHPQHGPHLKQNKVGTFNSVLAADLHLPRDPQGKTDFATLV
KQLKECPTLQDQADILYILNTSKGADWLVELSGPGQGGVSVHTLLEELYIQAGACKEWGL
IRYISGILRKRVEVLAEACTDLISHHKQLTVGLPPEPRERVITVPLPPEELNTLIYEASG
QDISVAVLTQEIMVYLAMYIRSQPALFGDMLRLRIGLIMQVMATELARSLHCSGEEASES
LMSLSPFDMKNLLHHILSGKEFGVERSMRPIQSTATSPAISIHEIGHTGATKTERTGIRK
LKSEIKQRCSSPSTPSGILSPVGPGPADGQLHWVERQGQWLRRRRLDGAINRVPVGFYQK
VWKILQKCHGLSIDGYVLPSSTTREMTAGEIKFAVQVESVLNHVPQPEYRQLLVESVMVL
GLVADVDVESIGSIIYVDRILHLANDLFLTDQKSYSAGDYFLEKDPETGICNFFYDSAPS
GIYGTMTYLSKAAVTYIQDFLPSSSCIMQ
>NEUI_FUGRU O42493 ISOTICIN-NEUROPHYSIN IT 1 PRECURSOR [CONTAINS: ISOTOCIN (IT)
; NEUROPHYSIN IT 1].
MTGTAISVCLLFLLSVCSACYISNCPIGGKRSIMDAPQRKCMSCGPGDRGRCFGPGICCG
ESFGCLMGSPESARCAEENYLLTPCQAGGRPCGSEGGLCASSGLCCDAESCTMDQSCLSE
EEGDERGSLFDGSDSGDVILKLLRLAGLTSPHQTH
>NEUV_FUGRU O42499 VASOTOCIN-NEUROPHYSIN VT 1 PRECURSOR [CONTAINS: VASOTOCIN (V
T); NEUROPHYSIN VT 1].
MPQCALLLSLLGLLALSSACYIQNCPRGGKRALPETGIRQCMSCGPRDRGRCFGPNICCG
EALGCLMGSPETARCAGENYLLTPCQAGGRPCGSEGGRCAVSGLCCNSESCAVDSDCLGE
TESLEPGDSSADSSPTELLLRLLHMSSRGQSEY

4.0 OUTPUT FILE FORMAT

   SEQSEARCH generates a domain hits file in FASTA-like format.
   DHF file (FASTA-like format)
   The file (Figure 1) contains two lines per hit. The first contains a
   description of the hit in 15 text tokens delimited by '^'. The tokens
   are as follows (a '.' is given where a token does not have a value):
   (i) Accession number of the hit.
   (ii) Database code from Uniprot.
   (iii - iv) Start and end positions of the hit relative to the full
   length sequence in the uniprot database (files of these type may also
   be generated by using SEQWORDS in which case a '.' will be given for
   these records - see SEQWORDS documentation ).
   (v) SCOP or CATH domain identifier code. This is a 7-character code
   that uniquely identifies the domain in SCOP or CATH.
   (vi) Domain identifier of the node. For example, if the domain
   alignment file was for a SCOP family, the SCOP Sunid for the family
   would be given. This number uniquely identifies the node (i.e. family
   in this case) in the raw SCOP or CATH parsable files.
   (vii) Domain class. Textual description of the 'Class' (SCOP and CATH
   domains).
   (viii) Domain architecture. Textual description of the 'Architecture'
   (CATH only).
   (ix) Domain topology. Textual description of the 'Topology' (CATH
   only).
   (x) Domain fold. Textual description of the 'Fold' (SCOP domains
   only).
   (xi) Domain superfamily. Textual description of the 'Superfamily'
   (SCOP and CATH domains).
   (xii) Domain family. Textual description of the 'Fold' (SCOP only).
   (xiii) Model type. The type of model that was used to generate the
   hit. May have a value of "PSIBLAST" (from PSIBLAST), "HMMER" (hidden
   Markov model from the HMMER package), "SAM" (hidden Markov model from
   the SAM package), SPARSE (sparse protein signature), HENIKOFF
   (Henikoff profile) or GRIBSKOV (Gribskov profile). A value of
   "PSIBLAST" is written by SEQSEARCH.
   (xiv) SC - Score of hit. A floating point value that is the score from
   psiblast (or other search algorithm).
   (xv) P-value of hit from search algorithm.
   (xvi) E-value of hit from search algorithm. The second line contains
   the protein sequence.

  Output files for usage example

  File: 54894.hits

CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
SI   54894
XX
NS   0
XX

  File: 55074.hits

CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
SI   55074
XX
NS   0
XX

  File: seqsearch.log

//
/ebi/services/idata/pmr/hgmp/test/data/structure/54894.salign
//
/ebi/services/idata/pmr/hgmp/test/data/structure/55074.salign

5.0 DATA FILES

   SEQSEARCH does not requires any data files.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
   -mode               menu       This option specifies the mode of SEQSEARCH
                                  operation. SEQSEARCH takes as input a
                                  directory of either i. single sequences, ii.
                                  set of sequences (unaligned or aligned, but
                                  typically aligned sequences within a domain
                                  alignment file)). The user has to specify
                                  which.
  [-inseqspath]        dirlist    This option specifies the location of
                                  sequences, e.g. DAF files (domain alignment
                                  files) (input). SEQSEARCH takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
  [-database]          string     Name of BLAST-indexed database to search.
   -niter              integer    This option specifies the number of PSIBLAST
                                  iterations. This option specifies the
                                  number of PSIBLAST iterations that are
                                  performed in a search.
   -evalue             float      This option specifies the threshold E-value
                                  for inclusion in family. This option
                                  specifies the threshold E-value for a
                                  PSIBLAST hit to be retained.
   -maxhits            integer    This option specifies the maximum number of
                                  hits. This option specifies the maximum
                                  number of PSIBLAST hit that are retained. It
                                  should normally be set high so that nothing
                                  is discarded.
  [-dhfoutdir]         outdir     This option specifies the location of DHF
                                  files (domain hits files) (output). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in FASTA format. The hits are
                                  relatives to a SCOP or CATH family and are
                                  found from a search of a sequence database.
                                  Files containing hits retrieved by PSIBLAST
                                  are generated by using SEQSEARCH.
   -logfile            outfile    This option specifies the name of log file
                                  for the build. The log file contains
                                  messages about any errors arising while
                                  SEQSEARCH ran.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory         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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   -mode This option specifies the mode of SEQSEARCH operation. SEQSEARCH
   takes as input a directory of either i. single sequences, ii. set of
   sequences (unaligned or aligned, but typically aligned sequences
   within a domain alignment file)). The user has to specify which.
   1 (Single sequences)
   2 (Multiple sequences (e.g. sequence set or alignment))
   1
   [-inseqspath]
   (Parameter 1) This option specifies the location of sequences, e.g.
   DAF files (domain alignment files) (input). SEQSEARCH takes as input a
   database of either i. single sequences, ii. sets of unaligned
   sequences or iii. sets of aligned sequences, e.g. a domain alignment
   file. A 'domain alignment file' contains a sequence alignment of
   domains belonging to the same SCOP or CATH family. The file is in
   clustal format annotated with domain family classification
   information. The files generated by using SCOPALIGN will contain a
   structure-based sequence alignment of domains of known structure only.
   Such alignments can be extended with sequence relatives (of unknown
   structure) by using SEQALIGN. Directory with files ./
   [-database]
   (Parameter 2) Name of BLAST-indexed database to search. Any string is
   accepted swissprot
   -niter This option specifies the number of PSIBLAST iterations. This
   option specifies the number of PSIBLAST iterations that are performed
   in a search. Any integer value 1
   -evalue This option specifies the threshold E-value for inclusion in
   family. This option specifies the threshold E-value for a PSIBLAST hit
   to be retained. Any numeric value 0.001
   -maxhits This option specifies the maximum number of hits. This option
   specifies the maximum number of PSIBLAST hit that are retained. It
   should normally be set high so that nothing is discarded. Any integer
   value 1000
   [-dhfoutdir]
   (Parameter 3) This option specifies the location of DHF files (domain
   hits files) (output). A 'domain hits file' contains database hits
   (sequences) with domain classification information, in FASTA format.
   The hits are relatives to a SCOP or CATH family and are found from a
   search of a sequence database. Files containing hits retrieved by
   PSIBLAST are generated by using SEQSEARCH. Output directory ./
   -logfile This option specifies the name of log file for the build. The
   log file contains messages about any errors arising while SEQSEARCH
   ran. Output file seqsearch.log
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of SEQSEARCH is shown below. Here is a
   sample session with seqsearch


% seqsearch 
Generate files of hits for families in a scop classification file by using
PSI-BLAST with seed alignments.
Name of scop classification file (embl format input): all.scop
Location of scop alignment files (input) [./]: structure
Extension of scop alignment files (input) [.salign]: 
Name of BLAST-indexed database to search [swissprot]: swnew
Number of PSIBLAST iterations [1]: 1
Threshold E-value for inclusion in family [0.001]: 0.001
Maximum number of hits [1000]: 100
Location of scop hits files (output) [./]: 
Extension of scop hits files (output) [.hits]: 
Name of log file for the build [seqsearch.log]: 
[blastpgp] WARNING: posFindAlignmentDimensions: Attempting to recover data from
 multiple alignment file

[blastpgp] WARNING: posProcessAlignment: Alignment recovered successfully

[blastpgp] WARNING: posFindAlignmentDimensions: Attempting to recover data from
 multiple alignment file

[blastpgp] WARNING: posProcessAlignment: Alignment recovered successfully


PROCESSING /ebi/services/idata/pmr/hgmp/test/data/structure/54894.salign
blastpgp -i ./seqsearch-1095239004.25358.seqin -B ./seqsearch-1095239004.25358.
seqsin -j 1 -e 0.001000 -b 100 -v 100 -d ../../data/swnew > ./seqsearch-1095239
004.25358.psiout

PROCESSING /ebi/services/idata/pmr/hgmp/test/data/structure/55074.salign
blastpgp -i ./seqsearch-1095239004.6149.seqin -B ./seqsearch-1095239004.6149.se
qsin -j 1 -e 0.001000 -b 100 -v 100 -d ../../data/swnew > ./seqsearch-109523900
4.6149.psiout


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

   All domain alignment files (with the file extension of .daf specified
   in the ACD file) were read from the directory /test_data; in this case
   two domain alignment files 54894.salign and 55074.salign were read.
   Sets of sequences extracted from these files were used to search the
   sequence database swissprot by using psiblast. psiblast was configured
   to perform 1 iteration with a threshold E-value for acceptance of a
   hit of 0.0001 and no more than 100 hits were generated from each
   iteration. Domain hits files were written to /test_data/seqsearch (
   the file extension .dhf was specified in the ACD file); in this case
   two files /test_data/54894.dhf and /test_data/55074.dhf were written.
   A log file called /test_data/seqsearch/seqsearch.log was also written.

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

   1. Use of psiblast
   psiblast must be installed on the system that is running SEQSEARCH.
   When running SEQSEARCH at the HGMP it is essential that the command
   'use blast_v2' (which runs the script /packages/menu/USE/blast_v2) is
   given before it is run.
   SEQSEARCH requires a blast-indexed database to be present, i.e. both
   the sequence and index file must be present on the system. The name of
   the database to search specified in the acd file is that which is
   given as the -d parameter to blastpgp (e.g. blastpgp -d swissprot).

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain hits file DHF format (FASTA-like format with domain
   classification information). Database hits (sequences) with domain
   classification information. The hits are relatives to a SCOP or CATH
   family and are found from a search of a sequence database. SEQSEARCH
   (hits retrieved by PSIBLAST) N.A.
   Domain alignment file DAF format (CLUSTAL-like format with domain
   classification information). Contains a sequence alignment of domains
   belonging to the same SCOP or CATH family. The file is annotated with
   domain family classification information. DOMAINALIGN (structure-based
   sequence alignment of domains of known structure). DOMAINALIGN
   alignments can be extended with sequence relatives (of unknown
   structure) to the family in question by using SEQALIGN.

   None

9.0 DESCRIPTION

   By using homology search tools such as blast it is possible to find
   relatives to a group of related proteins (family, superfamily etc),
   given one or more sequences belonging to the group of interest. For
   example, when using psiblast it is possible to use a sequence
   alignment as the seed with which to search a sequence database.
   Performing such searches for large datasets such as all families
   within SCOP or CATH potentially requires a lot of time for preparation
   of datasets, running jobs and so on, in addition to the compute time
   required for the searches themselves. SEQSEARCH automatically performs
   a psiblast search of a sequence database for each file in a directory
   of sequences or sets of sequences. These sequences are used for the
   searches. Typically, the directory contains DAF files (domain
   alignment files) and the alignments are for a certain node (e.g.
   family, superfamily etc) from SCOP or CATH.

10.0 ALGORITHM

   None.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   contactcount Counts specific versus non-specific contacts in a
   directory of cleaned protein chain contact files
   contacts Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of intra-chain residue-residue contact data
   domainalign Generates DAF files (domain alignment files) of
   structure-based sequence alignments for nodes in a DCF file (domain
   classification file)
   domainrep Reorder DCF file (domain classification file) so that the
   representative structure of each user-specified node is given first
   domainreso Removes low resolution domains from a DCF file (domain
   classification file)
   interface Reads CCF files (clean coordinate files) and writes CON
   files (contact files) of inter-chain residue-residue contact data
   libgen Generates various types of discriminating elements for each
   alignment in a directory
   psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style
   protein co-ordinate file
   rocon Reads a DHF file (domain hits file) of hits (sequences of
   unknown structural classification) and a DHF file of validation
   sequences (known classification) and writes a 'hits file' for the
   hits, which are classified and rank-ordered on the basis of score
   rocplot Provides interpretation and graphical display of the
   performance of discriminating elements (e.g. profiles for protein
   families). rocplot reads file(s) of hits from discriminator-database
   search(es), performs ROC analysis on the hits, and writes graphs
   illustrating the diagnostic performance of the discriminating elements
   seqalign Reads a DAF file (domain alignment file) and a DHF file
   (domain hits file) and writes a DAF file extended with the hits
   seqfraggle Removes fragments from DHF files (domain hits files) or
   other files of sequences
   seqsort Reads DHF files (domain hits files) of database hits
   (sequences) and removes hits of ambiguous classification
   seqwords Generates DHF files (domain hits files) of database hits
   (sequences) for nodes in a DCF file (domain classification file) by
   keyword search of UniProt
   siggen Generates a sparse protein signature from an alignment and
   residue contact data
   sigscan Generates a DHF file (domain hits file) of hits (sequences)
   from scanning a signature against a sequence database

12.0 DIAGNOSTIC ERROR MESSAGES

   The following 3 types of message might appear in the log file:
   WARN Could not open for reading my.file
   WARN No PSIBLAST hits therefore no output file my.file
   WARN Could not open for writing my.file

13.0 AUTHORS

   Ranjeeva Ranasinghe (rranasin@rfcgr.mrc.ac.uk)
   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
   Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.
   
   See also http://emboss.sourceforge.net/

  14.1 Other useful references

   Altschul et al, Nuc. Acids. Res. 25:3389-3402, 1997
