## 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-OXOGLUTARATE 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 GDP-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 (VT); 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-1095239004.25358.psiout

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