| ## SEQNR 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

Removes redundancy from DHF files (domain hits files) or other files of sequences

## 2.0 INPUTS & OUTPUTS

SEQNR removes redundancy from DHF files (domain hits files) or other files of sequences. A directory of DHF files (all sequences) is read and a directory of new DHF files (non-redundant sequences) plus (optionally) a second directory of DHF files (redundant sequences) is written. Optionally, up to two further directories of filter sequences may be read: these are considered in the redundancy calculation but never appear in the output files. Typically, one of the further directories contains DHF files each with a single sequence and the other DAF files (domain alignment files) each containing a sequence alignment, but any sequence(s) may be given. Each filter directory must contain a file for each file in main input directory and the files must have the same base name. For example, sequences from "family.dhf" and "family.daf" are considered for the input DHF file "family.hits".
Redundancy is removed at either (i) a user-defined threshold of sequence similarity or (ii) a user-defined range of threshold sequence similarity. Files of sequences in any supported format may be read and written (not just DHF or DAF files). A log file is also written.
The path for all files (input and output) are specified by the user. The file extensions are set in the ACD file. The name of the log file is set by the user.

## 3.0 INPUT FILE FORMAT

The format of the domain hits file is described in SEQSEARCH documentation.
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: scop.fam

    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   27
    XX
    NN   [1]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9YBD5
    XX
    RA   11 START; 105 END;
    XX
    SQ   SEQUENCE    95 AA;  10687 MW;  B8ACF34B CRC32;
         VRKIRSGVVI DHIPPGRAFT MLKALGLLPP RGYRWRIAVV INAESSKLGR KDILKIEGYK
         PRQRDLEVLG IIAPGATFNV IEDYKVVEKV KLKLP
    XX
    NN   [2]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9UX07
    XX
    RA   12 START; 104 END;
    XX
    SQ   SEQUENCE    93 AA;  10312 MW;  12DDDE7C CRC32;
         VSKIRNGTVI DHIPAGRALA VLRILGIRGS EGYRVALVMN VESKKIGRKD IVKIEDRVID
         EKEASLITLI APSATINIIR DYVVTEKRHL EVP
    XX
    NN   [3]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9KP65
    XX
    RA   9 START; 100 END;
    XX

      [Part of this file has been deleted for brevity]

         MMFHKIYIQK HDNVSILFAD IEGFTSLASQ CTAQELVMTL NELFARFDKL AAENHCLRIK
         ILGDCYYCVS GLPEARADHA HCCVEMGVDM IEAISLVREV TGVNVNMRVG IHSGRVHCGV
         LGLRKWQFDV WSNDVTLANH MEAGGRAGRI HITRATLQYL NGDYEVEPGR GGERNAYLKE
         QHIETFLIL
    XX
    NN   [111]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O30820
    XX
    RA   241 START; 400 END;
    XX
    SQ   SEQUENCE   160 AA;  17506 MW;  B1E1A024 CRC32;
         NIIADKYDEA SVLFADIVGF TERASSTAPA DLVRFLDRLY SAFDELVDQH GLEKIKVSGD
         SYMVVSGVPR PRPDHTQALA DFALDMTNVA AQLKDPRGNP VPLRVGLATG PVVAGVVGSR
         RFFYDVWGDA VNVASRMEST DSVGQIQVPD EVYERLKDDF
    XX
    NN   [112]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O19179
    XX
    RA   877 START; 1032 END;
    XX
    SQ   SEQUENCE   156 AA;  17212 MW;  675838EA CRC32;
         PEYFEEVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPQRNG QRHAAEIANM ALDILSAVGS FRMRHMPEVP VRIRIGLHSG PCVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVNM STVRIL
    XX
    NN   [113]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O02740
    XX
    RA   877 START; 1042 END;
    XX
    SQ   SEQUENCE   166 AA;  18151 MW;  E2BB2824 CRC32;
         PEGFDLVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPKRNG MRHAAEIANM SLDILSSVGT FKMRHMPEVP VRIRIGLHSG PVVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVSH STVTILRTLG EGYEVE
    XX
    //

### File: scop.oth

### File: all.scop2

    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   D1FX2A_
    XX
    EN   1FX2
    XX
    SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 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   Receptor-type monomeric adenylyl cyclase
    XX
    OS   Trypanosome (Trypanosoma brucei), different isoform
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   A CHAIN; . START; . END;
    //
    ID   D4AT1B1
    XX
    EN   4AT1
    XX
    SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
    XX
    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
    DO   Aspartate carbamoyltransferase
    XX
    OS   Escherichia coli
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   B CHAIN; 8 START; 100 END;
    //
    ID   D4AT1D1
    XX
    EN   4AT1
    XX
    SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
    XX
    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
    DO   Aspartate carbamoyltransferase
    XX
    OS   Escherichia coli
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   D CHAIN; 8 START; 100 END;
    //

## 4.0 OUTPUT FILE FORMAT

The format of the domain hits file is described in SEQSEARCH documentation.

### Output files for usage example

### File: famnr.hits

### File: scop.all

    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   27
    XX
    NN   [1]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    GP   NON_REDUNDANT
    XX
    AC   Q9YBD5
    XX
    RA   11 START; 105 END;
    XX
    SQ   SEQUENCE    95 AA;  10687 MW;  B8ACF34B CRC32;
         VRKIRSGVVI DHIPPGRAFT MLKALGLLPP RGYRWRIAVV INAESSKLGR KDILKIEGYK
         PRQRDLEVLG IIAPGATFNV IEDYKVVEKV KLKLP
    XX
    NN   [2]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    GP   NON_REDUNDANT
    XX
    AC   Q9UX07
    XX
    RA   12 START; 104 END;
    XX
    SQ   SEQUENCE    93 AA;  10312 MW;  12DDDE7C CRC32;
         VSKIRNGTVI DHIPAGRALA VLRILGIRGS EGYRVALVMN VESKKIGRKD IVKIEDRVID
         EKEASLITLI APSATINIIR DYVVTEKRHL EVP
    XX
    NN   [3]
    XX
    TY   HIT
    XX
    SC   0.00
    XX

      [Part of this file has been deleted for brevity]

    XX
    TY   HIT
    XX
    SC   0.00
    XX
    GP   NON_REDUNDANT
    XX
    AC   O30820
    XX
    RA   241 START; 400 END;
    XX
    SQ   SEQUENCE   160 AA;  17506 MW;  B1E1A024 CRC32;
         NIIADKYDEA SVLFADIVGF TERASSTAPA DLVRFLDRLY SAFDELVDQH GLEKIKVSGD
         SYMVVSGVPR PRPDHTQALA DFALDMTNVA AQLKDPRGNP VPLRVGLATG PVVAGVVGSR
         RFFYDVWGDA VNVASRMEST DSVGQIQVPD EVYERLKDDF
    XX
    NN   [112]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    GP   NON_REDUNDANT
    XX
    AC   O19179
    XX
    RA   877 START; 1032 END;
    XX
    SQ   SEQUENCE   156 AA;  17212 MW;  675838EA CRC32;
         PEYFEEVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPQRNG QRHAAEIANM ALDILSAVGS FRMRHMPEVP VRIRIGLHSG PCVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVNM STVRIL
    XX
    NN   [113]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    GP   NON_REDUNDANT
    XX
    AC   O02740
    XX
    RA   877 START; 1042 END;
    XX
    SQ   SEQUENCE   166 AA;  18151 MW;  E2BB2824 CRC32;
         PEGFDLVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPKRNG MRHAAEIANM SLDILSSVGT FKMRHMPEVP VRIRIGLHSG PVVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVSH STVTILRTLG EGYEVE
    XX
    //

### File: seqnr.log

    //
    54894
    No swissprot sequence for domain D4AT1B1 from alignment so no hit will be given in validation file
    No swissprot sequence for domain D4AT1D1 from alignment so no hit will be given in validation file
    Overlap between 2 SEEDs (acc. Not_available) from alignment file.
    //
    55074
    No swissprot sequence for domain D1CS4A_ from alignment so no hit will be given in validation file
    No swissprot sequence for domain D1FX2A_ from alignment so no hit will be given in validation file
    Overlap between 2 SEEDs (acc. Not_available) from alignment file.

## 5.0 DATA FILES

SEQNR requires a residue substitution matrix.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-dhfinpath]         dirlist    This option specifies the location of DHF
                                      files (domain hits files) (input). A 'domain
                                      hits file' contains database hits
                                      (sequences) with domain classification
                                      information, in the DHF format (FASTA or
                                      EMBL-like). 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.
       -[no]dosing         toggle     This option specifies whether to use singlet
                                      sequences (e.g. DHF files) to filter input.
                                      Optionally, up to two further directories
                                      of sequences may be read: these are
                                      considered in the redundancy calculation but
                                      never appear in the output files.
    *  -singletsdir        directory  This option specifies the location of
                                      singlet filter sequences (e.g. DHF files)
                                      (input). A 'domain hits file' contains
                                      database hits (sequences) with domain
                                      classification information, in the DHF
                                      format (FASTA or EMBL-like). 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.
       -[no]dosets         toggle     This option specifies whether to use sets of
                                      sequences (e.g. DHF files) to filter input.
                                      Optionally, up to two further directories
                                      of sequences may be read: these are
                                      considered in the redundancy calculation but
                                      never appear in the output files.
    *  -insetsdir          directory  This option specifies location of sets of
                                      filter sequences (e.g. DAF files) (input). 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.
       -mode               menu       This option specifies whether to remove
                                      redundancy at a single threshold % sequence
                                      similarity or remove redundancy outside a
                                      range of acceptable threshold % similarity.
                                      All permutations of pair-wise sequence
                                      alignments are calculated for each set of
                                      input sequences in turn using the EMBOSS
                                      implementation of the Needleman and Wunsch
                                      global alignment algorithm. Redundant
                                      sequences are removed in one of two modes as
                                      follows: (i) If a pair of proteins achieve
                                      greater than a threshold percentage sequence
                                      similarity (specified by the user) the
                                      shortest sequence is discarded. (ii) If a
                                      pair of proteins have a percentage sequence
                                      similarity that lies outside an acceptable
                                      range (specified by the user) the shortest
                                      sequence is discarded.
    *  -thresh             float      This option specifies the % sequence
                                      identity redundancy threshold. The %
                                      sequence identity redundancy threshold
                                      determines the redundancy calculation. If a
                                      pair of proteins achieve greater than this
                                      threshold the shortest sequence is
                                      discarded.
    *  -threshlow          float      This option specifies the % sequence
                                      identity redundancy threshold (lower limit).
                                      The % sequence identity redundancy
                                      threshold determines the redundancy
                                      calculation. If a pair of proteins have a
                                      percentage sequence similarity that lies
                                      outside an acceptable range the shortest
                                      sequence is discarded.
    *  -threshup           float      This option specifies the % sequence
                                      identity redundancy threshold (upper limit).
                                      The % sequence identity redundancy
                                      threshold determines the redundancy
                                      calculation. If a pair of proteins have a
                                      percentage sequence similarity that lies
                                      outside an acceptable range the shortest
                                      sequence is discarded.
      [-dhfoutdir]         outdir     This option specifies the location of DHF
                                      files (domain hits files) of non-redundant
                                      sequences (output). A 'domain hits file'
                                      contains database hits (sequences) with
                                      domain classification information, in the
                                      DHF format (FASTA or EMBL-like). 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.
       -dored              toggle     This option specifies whether to retain
                                      redundant sequences. If this option is set a
                                      DHF file (domain hits file) of redundant
                                      sequences is written.
    *  -redoutdir          outdir     This option specifies the location of DHF
                                      files (domain hits files) of redundant
                                      sequences (output). A 'domain hits file'
                                      contains database hits (sequences) with
                                      domain classification information, in the
                                      DHF format (FASTA or EMBL-like). 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 SEQNR log
                                      file (output). The log file contains
                                      messages about any errors arising while
                                      SEQNR ran.

       Additional (Optional) qualifiers:
       -matrix             matrixf    This option specifies the residue
                                      substitution matrix that is used for
                                      sequence comparison.
       -gapopen            float      This option specifies the gap insertion
                                      penalty. The gap insertion penalty is the
                                      score taken away when a gap is created. The
                                      best value depends on the choice of
                                      comparison matrix. The default value assumes
                                      you are using the EBLOSUM62 matrix for
                                      protein sequences, and the EDNAFULL matrix
                                      for nucleotide sequences.
       -gapextend          float      This option specifies the gap extension
                                      penalty. The gap extension, penalty is added
                                      to the standard gap penalty for each base
                                      or residue in the gap. This is how long gaps
                                      are penalized. Usually you will expect a
                                      few long gaps rather than many short gaps,
                                      so the gap extension penalty should be lower
                                      than the gap penalty. An exception is where
                                      one or both sequences are single reads with
                                      possible sequencing errors in which case
                                      you would expect many single base gaps. You
                                      can get this result by setting the gap open
                                      penalty to zero (or very low) and using the
                                      gap extension penalty to control gap
                                      scoring.

       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
--- | --- | ---
[-dhfinpath] (Parameter 1) | This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). 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. | Directory with files | ./
-[no]dosing | This option specifies whether to use singlet sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files. | Toggle value Yes/No | Yes
-singletsdir | This option specifies the location of singlet filter sequences (e.g. DHF files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). 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. | Directory | ./
-[no]dosets | This option specifies whether to use sets of sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files. | Toggle value Yes/No | Yes
-insetsdir | This option specifies location of sets of filter sequences (e.g. DAF files) (input). 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 | ./
-mode | This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded. |
1 | (Remove redundancy at a single threshold % sequence similarity)
2 | (Remove redundancy outside a range of acceptable threshold % similarity)
| 1
-thresh | This option specifies the % sequence identity redundancy threshold. The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded. | Any numeric value | 95.0
-threshlow | This option specifies the % sequence identity redundancy threshold (lower limit). The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. | Any numeric value | 30.0
-threshup | This option specifies the % sequence identity redundancy threshold (upper limit). The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. | Any numeric value | 90.0
[-dhfoutdir] (Parameter 2) | This option specifies the location of DHF files (domain hits files) of non-redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). 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 | ./
-dored | This option specifies whether to retain redundant sequences. If this option is set a DHF file (domain hits file) of redundant sequences is written. | Toggle value Yes/No | No
-redoutdir | This option specifies the location of DHF files (domain hits files) of redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). 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 SEQNR log file (output). The log file contains messages about any errors arising while SEQNR ran. | Output file | seqnr.log
Additional (Optional) qualifiers | Allowed values | Default
-matrix | This option specifies the residue substitution matrix that is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62
-gapopen | This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence
-gapextend | This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

### 6.2 EXAMPLE SESSION

An example of interactive use of SEQNR is shown below. Here is a sample session with seqnr

    % seqnr
    Reads a scop families file and a scop ambiguities file and writes (i) a
    non-redundant scop families file and (ii) a scop validation file.
    Name of the scop families file (input): scop.fam
    Name of ambiguities file (input): scop.oth
    Name of scop classification file (embl format input): all.scop2
    Location of scop alignment files (input) [./]:
    Extension of scop alignment files [.salign]:
    Number of overlapping residues required to define two hits as 'overlapping' [10]: 20
    The % sequence identity redundancy threshold [95.0]: 40
    Mode of operation
             1 : Validation file for signatures from structure-based sequence alignemnts (no scop families file)
             2 : Validation file for signatures from extended alignments (plus non-redundant scop families file)
    Select mode [1]:
    Name of scop validation file (output) [all.hits]: scop.all
    Name seqnr log file (output) [seqnr.log]: seqnr.log
    Warning: Sequence length smaller than overlap limit in embDmxScophitsOverlapAcc ... checking for string match instead
    Warning: 2 domains in the alignment share the same accession number and overlap.
    Only one will be given in the validation file.
    Warning: Sequence length smaller than overlap limit in embDmxScophitsOverlapAcc ... checking for string match instead
    Warning: Zero length sequence in SeqsetNR
    Warning: Sequence length smaller than overlap limit in embDmxScophitsOverlapAcc ... checking for string match instead
    Warning: 2 domains in the alignment share the same accession number and overlap.
    Only one will be given in the validation file.
    Warning: Sequence length smaller than overlap limit in embDmxScophitsOverlapAcc ... checking for string match instead
    Warning: Zero length sequence in SeqsetNR

    Processing 54894
    Processing 55074

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

Two domains within the same family are classified as redundant if they share at least 40% sequence similarity; the default residue substitution matrix EBLOSUM62 and default gap insertion and extension penalties were used for the alignments.

## 7.0 KNOWN BUGS & WARNINGS

None.

## 8.0 NOTES

None.

### 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

Redundancy in a database or other collection of sequences occurs when one or more similar sequences are present. The inclusion of very similar sequences in certain analyses will introduce undesirable bias. For example, a family may possess 100 sequences in the sequence database, but 90 of these might be essentially the same sequence, e.g. very close relatives or mutations of a single sequence. Although 100 sequences are known, the family only contains 11 sequences that are essentially unique. For many applications it is desirable or even essential to remove redundant sequences from a set in order to produce a smaller set that is representative of the whole. SEQNR removes redundancy from an input file of sequences, either at a single threshold of sequence similiarty (e.g. 40%) or within a threshold range of sequence similiarty (e.g. 40% - 70%).

## 10.0 ALGORITHM

Redundancy is calculated for each DHF file in the input directory in turn. The procedure is as follows. 1. Create a list of sequences from the main input directory. 2. Add sequences from both filter directories (if specified) to list but mark them up (they are considered in the redundancy calculation but never appear in the output files). 3. Identify redundant domains. 4. Write non-redundant domains to main output directory. 5. If specified, write redundant domains to output directory.

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
aaindexextract | Extract data from AAINDEX
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values
cathparse | Reads raw CATH classification files and writes DCF file (domain classification file)
cutgextract | Extract data from CUTG
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file)
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS
domainseqs | Adds sequence records to a DCF file (domain classification file)
domainsse | Adds secondary structure records to a DCF file (domain classification file)
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format
pdbparse | Parses PDB files and writes CCF files (clean coordinate files) for proteins
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format
printsextract | Extract data from PRINTS
prosextract | Builds the PROSITE motif database for patmatmotifs to search
rebaseextract | Extract data from REBASE
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file)
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file)
ssematch | Searches a DCF file (domain classification file) for secondary structure matches
tfextract | Extract data from TRANSFAC

## 12.0 DIAGNOSTIC ERROR MESSAGES

The log file might contain the following messages:
embHitlistReadFasta call failed in seqnr (By default SEQNR expects a domain hits file in the main input directory and the first (singlets) filter directory. This message is given if some other type of sequence file is given. Its not really an error, just a warning).
Empty input file my.file (This is given if the main input file 'my.file' did not contain any sequences. No output file is generated for this file.)
Empty singlets filter file my.file (This is given if the singlets filter file 'my.file' did not contain any sequences. An output file is still generated for this file.)
Empty sets filter file my.file (This is given if the sets filter file 'my.file' did not contain any sequences. An output file is still generated for this file.)
ajDmxScopalgRead call failed in seqnr my.file (By default SEQNR expects a domain alignment file in the second (sets) filter directory. This message is given if some other type of sequence sets file (called 'my.file') is given. Its not really an error, just a warning).

## 13.0 AUTHORS

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