EMBOSS: skipredundant

| skipredundant

## Function

Remove redundant sequences from an input set

## 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%).

## Algorithm

Redundancy is calculated for each pair of sequences in turn.

## Usage

Here is a sample session with skipredundant

    % skipredundant -threshold 80 -keepredundant
    Remove redundant sequences from an input set
    Input sequence set: globins.fasta
    Redundancy removal options
             1 : Single threshold percentage sequence similarity
             2 : Outside a range of acceptable threshold percentage similarities
    Select number [1]:
    Gap opening penalty [10.0]:
    Gap extension penalty [0.5]:
    output sequence(s) [globins.keep]:
    Second output sequence(s) [globins.redundant]:

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

## Command line arguments

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-sequences]         seqset     Sequence set filename and optional format,
                                      or reference (input USA)
       -mode               menu       [1] This option specifies whether to remove
                                      redundancy at a single threshold percentage
                                      sequence similarity or remove redundancy
                                      outside a range of acceptable threshold
                                      percentage 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. (Values: 1 (Single
                                      threshold percentage sequence similarity); 2
                                      (Outside a range of acceptable threshold
                                      percentage similarities))
    *  -threshold          float      [95.0] This option specifies the percentage
                                      sequence identity redundancy threshold. The
                                      percentage 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)
    *  -minthreshold       float      [30.0] This option specifies the percentage
                                      sequence identity redundancy threshold
                                      (lower limit). The percentage 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)
    *  -maxthreshold       float      [90.0] This option specifies the percentage
                                      sequence identity redundancy threshold
                                      (upper limit). The percentage 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)
       -gapopen            float      [10.0 for any sequence] The gap open 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)
       -gapextend          float      [0.5 for any sequence] 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)
      [-outseq]            seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)
      [-redundantoutseq]   seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers:
       -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                      This is the scoring matrix file used when
                                      comparing sequences. By default it is the
                                      file 'EBLOSUM62' (for proteins) or the file
                                      'EDNAFULL' (for nucleic sequences). These
                                      files are found in the 'data' directory of
                                      the EMBOSS installation.

       Advanced (Unprompted) qualifiers:
       -feature            toggle     Sequence feature information will be
                                      retained if this option is set.
       -keepredundant      toggle     [N] This option specifies whether to retain
                                      redundant sequences. If this option is set a
                                      file of redundant sequences is written.

       Associated qualifiers:

       "-sequences" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outseq" associated qualifiers
       -osformat2          string     Output seq format
       -osextension2       string     File name extension
       -osname2            string     Base file name
       -osdirectory2       string     Output directory
       -osdbname2          string     Database name to add
       -ossingle2          boolean    Separate file for each entry
       -oufo2              string     UFO features
       -offormat2          string     Features format
       -ofname2            string     Features file name
       -ofdirectory2       string     Output directory

       "-redundantoutseq" associated qualifiers
       -osformat3          string     Output seq format
       -osextension3       string     File name extension
       -osname3            string     Base file name
       -osdirectory3       string     Output directory
       -osdbname3          string     Database name to add
       -ossingle3          boolean    Separate file for each entry
       -oufo3              string     UFO features
       -offormat3          string     Features format
       -ofname3            string     Features file name
       -ofdirectory3       string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequences] (Parameter 1) | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
-mode | This option specifies whether to remove redundancy at a single threshold percentage sequence similarity or remove redundancy outside a range of acceptable threshold percentage 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 | (Single threshold percentage sequence similarity)
2 | (Outside a range of acceptable threshold percentage similarities)
| 1
-threshold | This option specifies the percentage sequence identity redundancy threshold. The percentage 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
-minthreshold | This option specifies the percentage sequence identity redundancy threshold (lower limit). The percentage 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
-maxthreshold | This option specifies the percentage sequence identity redundancy threshold (upper limit). The percentage 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
-gapopen | The gap open 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 | 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
[-outseq] (Parameter 2) | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
[-redundantoutseq] (Parameter 3) | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
-datafile | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
Advanced (Unprompted) qualifiers | Allowed values | Default
-feature | Sequence feature information will be retained if this option is set. | Toggle value Yes/No | No
-keepredundant | This option specifies whether to retain redundant sequences. If this option is set a file of redundant sequences is written. | Toggle value Yes/No | No

## Input file format

skipredundant reads any normal sequence USAs.

### Input files for usage example

### File: globins.fasta

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR
    >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
    VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
    LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
    GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY
    >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
    GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
    QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
    VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

## Output file format

skipredundant outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

### Output files for usage example

### File: globins.keep

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
    VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
    LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
    GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY
    >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
    GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
    QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
    VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

### File: globins.redundant

    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR

## Data files

For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used. Others can be specified.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
aligncopy | Reads and writes alignments
aligncopypair | Reads and writes pairs from alignments
biosed | Replace or delete sequence sections
codcopy | Copy and reformat a codon usage table
cutseq | Removes a section from a sequence
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences
descseq | Alter the name or description of a sequence
entret | Retrieves sequence entries from flatfile databases and files
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from sequence(s)
extractseq | Extract regions from a sequence
featcopy | Reads and writes a feature table
featreport | Reads and writes a feature table
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Create random nucleotide sequences
makeprotseq | Create random protein sequences
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N
maskambigprot | Masks all ambiguity characters in protein sequences with X
maskfeat | Write a sequence with masked features
maskseq | Write a sequence with masked regions
newseq | Create a sequence file from a typed-in sequence
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn | Remove carriage return from ASCII files
nospace | Remove all whitespace from an ASCII text file
notab | Replace tabs with spaces in an ASCII text file
notseq | Write to file a subset of an input stream of sequences
nthseq | Write to file a single sequence from an input stream of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a nucleotide sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads sequences and writes them to individual files
sizeseq | Sort sequences by size
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split sequence(s) into smaller sequences
trimest | Remove poly-A tails from nucleotide sequences
trimseq | Remove unwanted characters from start and end of sequence(s)
trimspace | Remove extra whitespace from an ASCII text file
union | Concatenate multiple sequences into a single sequence
vectorstrip | Removes vectors from the ends of nucleotide sequence(s)
yank | Add a sequence reference (a full USA) to a list file

## Author(s)

Jon Ison (jison © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None