| splitter

## Function

Split a sequence into (overlapping) smaller sequences

## Description

This simple editing program allows you to split a long sequence into smaller, optionally overlapping, subsequences.

There should be little requirement to split sequences into smaller sub-sequences in EMBOSS, but there may be circumstances where memory usage becomes restrictive when dealing with truly large sequences. In this case, memory usage may be reduced by repeating the analysis several times on split sub-sequences.

If you need to split a large sequence into smaller subsequences so that a non-EMBOSS program can analyse the smaller sequence, it may also be useful to write the sub-sequences into separate files instead of the default EMBOSS behaviour of concatenating them together into one file.

To write the output sequences to separate files, use the command-line switch '-ossingle'.

## Usage

Here is a sample session with splitter

Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences:

    % splitter tembl:AP000504 ap000504.split
    Split a sequence into (overlapping) smaller sequences

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

Example 2

Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence:

    % splitter tembl:AP000504 ap000504.split -size=50000 -over=3000
    Split a sequence into (overlapping) smaller sequences

Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers:
       -size               integer    Size to split at
       -overlap            integer    Overlap between split sequences

       Advanced qualifiers:
       -addoverlap         boolean    Add overlap to size

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outseq" related 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

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
-size | Size to split at | Integer 1 or more | 10000
-overlap | Overlap between split sequences | Integer 0 or more | 0
Advanced qualifiers | Allowed values | Default
-addoverlap | Add overlap to size | Boolean value Yes/No | No

## Input File Format

splitter reads one or more sequence USAs.

### Input files for usage example

'tembl:AP000504' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:AP000504

    ID   AP000504   standard; DNA; HUM; 100000 BP.
    XX
    AC   AP000504; BA000025;
    XX
    SV   AP000504.1
    XX
    DT   28-SEP-1999 (Rel. 61, Created)
    DT   22-AUG-2001 (Rel. 68, Last updated, Version 3)
    XX
    DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section
    DE   3/20.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-100000
    RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
    RT   ;
    RL   Submitted (21-SEP-1999) to the EMBL/GenBank/DDBJ databases.
    RL   Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced
    RL   Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan
    RL   (E-mail:mika@tokyo.jst.go.jp, URL:http://www-alis.tokyo.jst.go.jp/,
    RL   Tel:81-3-5214-8491, Fax:81-3-5214-8470)
    XX
    RN   [2]
    RA   Shiina S., Tamiya G., Oka A., Inoko H.;
    RT   "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region";
    RL   Unpublished.
    XX
    DR   SWISS-PROT; O00299; CLI1_HUMAN.
    DR   SWISS-PROT; O43196; MSH5_HUMAN.
    DR   SWISS-PROT; O95445; APOM_HUMAN.
    DR   SWISS-PROT; O95865; DDH2_HUMAN.
    DR   SWISS-PROT; O95867; NG24_HUMAN.
    DR   SWISS-PROT; P13862; KC2B_HUMAN.
    XX
    CC   This sequence is conducted by Tokai University as a JST sequencing
    CC   Team.
    CC   Principal Investigator: Hidetoshi Inoko Ph.D
    CC   Phone:+81-463-93-1121, Fax:+81-463-94-8884,
    CC   The sequence is submitted by Human Genome Sequencing in ALIS
    CC   project of JST
    CC   Japan Science and Technology Corporation (JST)
    CC   5-3, Yonbancyo, Chiyoda-ku, Tokyo, 102-0081 Japan
    CC   For further infomation about this sequences, please visit our
    CC   sequence archive Web site (http://www-alis.tokyo.jst.go.jp/HGS/top.

      [Part of this file has been deleted for brevity]

         gggtggatca tgaggtcaag agatcgagac tatcctggct aacatgatga aaccccgtct     97080
         ctactaaaaa tacaaaaaat tagctgggca tggtggcggg cacctgtagt cccagctact     97140
         cgggaggctg agtcaggaga atggtgtgaa cccaggagac ggagcttgca gtgagctgag     97200
         gtcgcaccac tgcactccag cctgggtgat agagcgagac tctgtctcaa aaaaaaaaaa     97260
         aaaaaaaaaa aaaacaaaaa ttagccgggt gtggtggcag gcaacttaat cccagctact     97320
         tgggaggcag aggcaggaga atcgtttgaa cctgggaggc ggaggttgaa gagaatagaa     97380
         gctctgctgg tccagagaag gattgggcca gggctctggg agaccaggga gaaagagggc     97440
         acatgtggtc cctgttgact gtgagggtgg gaatctgagg aaggctttgg ctcattgccc     97500
         cttgggtttg tccacagcca tccttcccct gcggagtatg tcgaggtgct ccaggagcta     97560
         cagcggctgg agagtcgcct ccagcccttc ttgcagcgct actacgaggt tctgggtgct     97620
         gctgccacca cggactacaa taacaatgtg agccctttga tggccctgcc ctttctcctc     97680
         agccccagta ctcccaaaac agaacaggct gaaatacaga taactctttc cctccctgga     97740
         aaaacattgc aacagggcca ggtgcagtgg ctcacgcctg taatcccagc actttgggag     97800
         gccaaggtgg gcggatcatc tgagatcggg agtttgagac cagcctggcc aacatggtgc     97860
         aaccccatct ctactgaaaa tataaacatt agctggatgt agtggtgcac acctgtaatc     97920
         ccagctactc aggaggctga ggcaggagaa tcgctagaac tcgggaggag ggggttgcag     97980
         tgagccgaga ttgcactact gcactctagc ctgggtgaca gagcgagact gtctcaaaaa     98040
         acaaaacaaa acaaaaaaac acacattgca acaaaacaat ttctctctaa acctgtaagt     98100
         gattttgtcc tcccttacag agaaggtgat aatctttgct gtaagcactg tcctcgtatc     98160
         gtaccccttg tgcccctgaa tgaatttaga aaatgtaaag tacaggagat cagtatatga     98220
         tgacttactg attcatagta gtgttttaat aggatgttcc ttatgtgaat aagatataat     98280
         ttatttgcaa agatttggtc tacatgtaaa cttccaagga tataactgaa agttttggag     98340
         gacatggtat tctcagtagg cattattgct tttattagtg agatggactc cagcttgata     98400
         ttttctgcct ttttgtgttt ggctggttgt gcgcagcacg agggccggga ggaggatcag     98460
         cggttgatca acttggtagg ggagagcctg cgactgctgg gcaacacctt tgttgcactg     98520
         tctgacctgc gctgcaatct ggcctgcacg cccccacgac acctgcatgt ggtccggcct     98580
         atgtctcact acaccacccc catggtgctc cagcaggcag ccattcccat acaggtgggt     98640
         tagggggagt ctggcctgag ggagagtgag gggtgttgat agagtgaccc agggtagcta     98700
         ctgggcctga aggaggttag gaaaggagga gactggaaac atggtgatga aggctggaga     98760
         tactttagag gtttatcatg aggttttctt ggttaggctc ttgtattttt ctcacatctg     98820
         cctgtccatc tgtctttttc agatcaatgt gggaaccact gtgaccatga caggaaatgg     98880
         gactcggccc cccccaactc ccaatgcaga ggcacctccc cctggtcctg ggcaggcctc     98940
         atccgtggct ccgtcttcta ccaatgtcga gtcctcagct gagggggctc ccccgccagg     99000
         tccagctccc ccgccagcca ccagccaccc gagggtcatc cggatttccc accagagtgt     99060
         ggaacccgtg gtcatgatgc acatgaacat tcaaggtgag aatagttgct ggcgagaaga     99120
         gcaggatcag catgatgagg gaggttcatg ctgaggtgtg agggaacagg gtggggaagg     99180
         gagaggcaca tgctggtggt ggtagcctgg ggaccagagc agaagcttaa gtagacagat     99240
         gtggggggtg tgggggttgg tttgtctttg gaggtgtgtt tgtgtggtga agggagtacc     99300
         tctccctgtt tagatggagg gaaaggcagg ctttctgatt gggggattat gggcctgaag     99360
         tatgcctgat ctcagaagga tatagttagg ccttggccct acctacctca gggccactgt     99420
         ctctgtctcc ctgcccagat tctggcacac agcctggtgg tgttccgagt gctcccactg     99480
         gccccctggg accccctggt catggccaaa ccctgggtaa gagtgagggc atcagggcag     99540
         gctgagctct gggtagagaa agggaagggc tgagtgggtg ggttgaaggg gtccaggttc     99600
         aaggttacat cagacccgcc ccccaggctc caccctcatc cagctgccct ccctgccccc     99660
         tgagttcatg cacgccgtcg cccaccagat cactcatcag gccatggtgg cagctgttgc     99720
         ctccgcggcc gcaggtaatg acctggaagg ggaggcttgg gaggtagggc acagtccatg     99780
         gtggcagctg gctggcaagg gcctggccct cagccctctt cggtctgtct cttctgccac     99840
         ccacaggaca gcaggtgcca ggcttcccaa cagctccaac ccgggtggtg attgcccggc     99900
         ccactcctcc acaggctcgg ccttcccatc ctggagggcc cccagtctct gggacactgg     99960
         tgagcaaggg tcggggagtt ctagtgcgta acagtctagg                          100000
    //

## Output File Format

### Output files for usage example

### File: ap000504.split

    >AP000504_1-10000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
    gaccaatctcactgtgaggaggcagtcaaagggaataatggaagagaggaagaggatttt
    ctcagtggcagtcatggcgtctgggatgaaggagtagtttccagaaaggaggcgttgttt
    gcttatctccagacctatttgagggaggcaagcaaagggaacggtcttgtagctcaattt
    tttcaccccattttaagaatgagacaatagaagcaagagagattatttgacttgcccaag
    ctcacacaggcagttaatggaaagctagagcaagaaccaaattttcagactcttagtcta
    attctctttttattctacatataatataaagatacttgtctgaaagcacagcctgagaaa
    gataaatggctgaggaaagtagacatctgtctggaattgaggattttggtcaaaataatg
    gtattaatagaactagtaacactaatgccttaatatctaattaggatagtacactcctgt
    tcttattgtaaacctaggaaagttatagaagtgccttatggatcataataagggtcactg
    aggcagtgccttttggtttggtgataaaaggctttaacttaatggggagaattccaacaa
    taaaaccctgtccaaaaagtgtcaccactcctcaggggaggccctcatccctagacatga
    cttaagcagaggcttcccaataagctgcaggttattaaagggtagggagcaggagagatc
    ttggggggacaggtcatagggcatgaggagcacaaaggtttaggatgacataaggcagag
    gggagatctgtgatgatgaaggtagagttgggggaaagaatgggacaccggaacagggag
    ttaggcaaagcaaaaggaaggagataccaaaatccacacttggcaaaaatatgatttcag
    gtcttttaggctctctgtgctcctgggaggctgtgggggaggaaagaaaaggctatcatt
    ctttacatctcagtccttctacctctgtctgacactccctctcacccaattctagccccc
    tggaatattccatatattagtccttccccattttccctctatcctttaccaagtccttac
    caagctttcccagaaatcgagtcatattctcatcctgtttggcactcgtaacaacagact
    ggggattgatctcatccagaacttggaaggagaacagagatcaaatgagttaaaggatct
    ttgtctttgactaagagaaaacccatagccctcctcttcctacccctctccttctcaaaa
    acatttcctccctaggagtagggagtgctctgcacagtgggaacacaggtagaagttgag
    atttagaaaagtagttaagagtggtgggatggtgagagggaagtgggatgttctggatgt
    tgtcactaggctgtaaacccctggagaacagacatgactgatttgcccagggctgaatct
    gaagcacctgaaacattgtaaatacgtcatatatatttgtggccaggcacagtggctcat
    gcctataatccctgccctttgggaggccaaggcaggcagatcactggaggccaggagctc
    aagacaagcctagccaacgtggtgaaaccctgcctctactaaaaatataaaaattagcca
    ggcgtgatggcagattcttgtaatcccagctactcgggagactgaggcaggagaattgct
    tgaatccgggagacggaggttgcagtgagccaagatggcaccactacacttccagcctga
    gtgacggagcaagacactgtctcaaaaaagaacaaccaaacaaaccaaaaaacagcctca
    caaatatttgttaaataatgaaatgaattcataaaaacaaaagagggagcctctgtgaag
    caactgtaaaatatattgagtcagtgctatagtttggatgtgatttgtccctgccaaata
    tcgtgttgaaatttaatccccagtgtgatagtgttgtgaggtagggcctagcaggaggtg
    tgtgggtgatgggagtggatcgctcatgaacagattaatgcccttcctggagtgtgttgg
    tgggtatgagtgagaggttctcactctattagttcctgagagagctggttgtcaaaaaga
    gcctggcatctccctcccccttgcttcttctctgccatgtgacctctacacaccctgcct
    tcccttcttccatgagttgaagcagtctgaggctctcaccagtgaagatgcccaattttg
    agctttccaaccatccagaaccataagccaaataaaactttttttttttttttaacaaat
    tactcagagtcaggtatttccttacagcaacacaaaatatgctagacagtgaggtgagtt
    aatgtaagtaaaacatggctgggcgtggtgactcacacctgtagtcccagcactttagga
    ggccaaggtgggcggatcacaaggtcaggagtttgagaccaccctggccaacatggtgaa
    acaccgtctgtgctaaaaacacacacaaaaaactagctgggtgtggtggcacacgcctgt
    agtcccagctactcgggaggttgagtcaggagaattgcttgaacccaggaggtggaggct
    gcagtgagccaagattgcgccactgcacttgagcctgggtaacagagcaagactctgtct
    agaaaaaaaaaatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg
    taacacatctgcaatcccagagagcagaggaattcatggttccatccccacctctctgga
    gaagcttgaggctctcgtggtctggggcatctggcatgaagtggatagtggagtcactag
    tatcatagtaggcaatgcccaagtatcctgaattccacagcacacacagatggatctgtc
    cagcaaggaagaaaggaaatcactattagaatcactcataagtgtagggtttaccatgtc

      [Part of this file has been deleted for brevity]

    aaatacaggccgggcacagtggctcacgcctgtaatcccagcactttgggaggccgaggc
    gggtggatcatgaggtcaagagatcgagactatcctggctaacatgatgaaaccccgtct
    ctactaaaaatacaaaaaattagctgggcatggtggcgggcacctgtagtcccagctact
    cgggaggctgagtcaggagaatggtgtgaacccaggagacggagcttgcagtgagctgag
    gtcgcaccactgcactccagcctgggtgatagagcgagactctgtctcaaaaaaaaaaaa
    aaaaaaaaaaaaaacaaaaattagccgggtgtggtggcaggcaacttaatcccagctact
    tgggaggcagaggcaggagaatcgtttgaacctgggaggcggaggttgaagagaatagaa
    gctctgctggtccagagaaggattgggccagggctctgggagaccagggagaaagagggc
    acatgtggtccctgttgactgtgagggtgggaatctgaggaaggctttggctcattgccc
    cttgggtttgtccacagccatccttcccctgcggagtatgtcgaggtgctccaggagcta
    cagcggctggagagtcgcctccagcccttcttgcagcgctactacgaggttctgggtgct
    gctgccaccacggactacaataacaatgtgagccctttgatggccctgccctttctcctc
    agccccagtactcccaaaacagaacaggctgaaatacagataactctttccctccctgga
    aaaacattgcaacagggccaggtgcagtggctcacgcctgtaatcccagcactttgggag
    gccaaggtgggcggatcatctgagatcgggagtttgagaccagcctggccaacatggtgc
    aaccccatctctactgaaaatataaacattagctggatgtagtggtgcacacctgtaatc
    ccagctactcaggaggctgaggcaggagaatcgctagaactcgggaggagggggttgcag
    tgagccgagattgcactactgcactctagcctgggtgacagagcgagactgtctcaaaaa
    acaaaacaaaacaaaaaaacacacattgcaacaaaacaatttctctctaaacctgtaagt
    gattttgtcctcccttacagagaaggtgataatctttgctgtaagcactgtcctcgtatc
    gtaccccttgtgcccctgaatgaatttagaaaatgtaaagtacaggagatcagtatatga
    tgacttactgattcatagtagtgttttaataggatgttccttatgtgaataagatataat
    ttatttgcaaagatttggtctacatgtaaacttccaaggatataactgaaagttttggag
    gacatggtattctcagtaggcattattgcttttattagtgagatggactccagcttgata
    ttttctgcctttttgtgtttggctggttgtgcgcagcacgagggccgggaggaggatcag
    cggttgatcaacttggtaggggagagcctgcgactgctgggcaacacctttgttgcactg
    tctgacctgcgctgcaatctggcctgcacgcccccacgacacctgcatgtggtccggcct
    atgtctcactacaccacccccatggtgctccagcaggcagccattcccatacaggtgggt
    tagggggagtctggcctgagggagagtgaggggtgttgatagagtgacccagggtagcta
    ctgggcctgaaggaggttaggaaaggaggagactggaaacatggtgatgaaggctggaga
    tactttagaggtttatcatgaggttttcttggttaggctcttgtatttttctcacatctg
    cctgtccatctgtctttttcagatcaatgtgggaaccactgtgaccatgacaggaaatgg
    gactcggccccccccaactcccaatgcagaggcacctccccctggtcctgggcaggcctc
    atccgtggctccgtcttctaccaatgtcgagtcctcagctgagggggctcccccgccagg
    tccagctcccccgccagccaccagccacccgagggtcatccggatttcccaccagagtgt
    ggaacccgtggtcatgatgcacatgaacattcaaggtgagaatagttgctggcgagaaga
    gcaggatcagcatgatgagggaggttcatgctgaggtgtgagggaacagggtggggaagg
    gagaggcacatgctggtggtggtagcctggggaccagagcagaagcttaagtagacagat
    gtggggggtgtgggggttggtttgtctttggaggtgtgtttgtgtggtgaagggagtacc
    tctccctgtttagatggagggaaaggcaggctttctgattgggggattatgggcctgaag
    tatgcctgatctcagaaggatatagttaggccttggccctacctacctcagggccactgt
    ctctgtctccctgcccagattctggcacacagcctggtggtgttccgagtgctcccactg
    gccccctgggaccccctggtcatggccaaaccctgggtaagagtgagggcatcagggcag
    gctgagctctgggtagagaaagggaagggctgagtgggtgggttgaaggggtccaggttc
    aaggttacatcagacccgccccccaggctccaccctcatccagctgccctccctgccccc
    tgagttcatgcacgccgtcgcccaccagatcactcatcaggccatggtggcagctgttgc
    ctccgcggccgcaggtaatgacctggaaggggaggcttgggaggtagggcacagtccatg
    gtggcagctggctggcaagggcctggccctcagccctcttcggtctgtctcttctgccac
    ccacaggacagcaggtgccaggcttcccaacagctccaacccgggtggtgattgcccggc
    ccactcctccacaggctcggccttcccatcctggagggcccccagtctctgggacactgg
    tgagcaagggtcggggagttctagtgcgtaacagtctagg

### Output files for usage example 2

### File: ap000504.split

    >AP000504_1-50000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
    gaccaatctcactgtgaggaggcagtcaaagggaataatggaagagaggaagaggatttt
    ctcagtggcagtcatggcgtctgggatgaaggagtagtttccagaaaggaggcgttgttt
    gcttatctccagacctatttgagggaggcaagcaaagggaacggtcttgtagctcaattt
    tttcaccccattttaagaatgagacaatagaagcaagagagattatttgacttgcccaag
    ctcacacaggcagttaatggaaagctagagcaagaaccaaattttcagactcttagtcta
    attctctttttattctacatataatataaagatacttgtctgaaagcacagcctgagaaa
    gataaatggctgaggaaagtagacatctgtctggaattgaggattttggtcaaaataatg
    gtattaatagaactagtaacactaatgccttaatatctaattaggatagtacactcctgt
    tcttattgtaaacctaggaaagttatagaagtgccttatggatcataataagggtcactg
    aggcagtgccttttggtttggtgataaaaggctttaacttaatggggagaattccaacaa
    taaaaccctgtccaaaaagtgtcaccactcctcaggggaggccctcatccctagacatga
    cttaagcagaggcttcccaataagctgcaggttattaaagggtagggagcaggagagatc
    ttggggggacaggtcatagggcatgaggagcacaaaggtttaggatgacataaggcagag
    gggagatctgtgatgatgaaggtagagttgggggaaagaatgggacaccggaacagggag
    ttaggcaaagcaaaaggaaggagataccaaaatccacacttggcaaaaatatgatttcag
    gtcttttaggctctctgtgctcctgggaggctgtgggggaggaaagaaaaggctatcatt
    ctttacatctcagtccttctacctctgtctgacactccctctcacccaattctagccccc
    tggaatattccatatattagtccttccccattttccctctatcctttaccaagtccttac
    caagctttcccagaaatcgagtcatattctcatcctgtttggcactcgtaacaacagact
    ggggattgatctcatccagaacttggaaggagaacagagatcaaatgagttaaaggatct
    ttgtctttgactaagagaaaacccatagccctcctcttcctacccctctccttctcaaaa
    acatttcctccctaggagtagggagtgctctgcacagtgggaacacaggtagaagttgag
    atttagaaaagtagttaagagtggtgggatggtgagagggaagtgggatgttctggatgt
    tgtcactaggctgtaaacccctggagaacagacatgactgatttgcccagggctgaatct
    gaagcacctgaaacattgtaaatacgtcatatatatttgtggccaggcacagtggctcat
    gcctataatccctgccctttgggaggccaaggcaggcagatcactggaggccaggagctc
    aagacaagcctagccaacgtggtgaaaccctgcctctactaaaaatataaaaattagcca
    ggcgtgatggcagattcttgtaatcccagctactcgggagactgaggcaggagaattgct
    tgaatccgggagacggaggttgcagtgagccaagatggcaccactacacttccagcctga
    gtgacggagcaagacactgtctcaaaaaagaacaaccaaacaaaccaaaaaacagcctca
    caaatatttgttaaataatgaaatgaattcataaaaacaaaagagggagcctctgtgaag
    caactgtaaaatatattgagtcagtgctatagtttggatgtgatttgtccctgccaaata
    tcgtgttgaaatttaatccccagtgtgatagtgttgtgaggtagggcctagcaggaggtg
    tgtgggtgatgggagtggatcgctcatgaacagattaatgcccttcctggagtgtgttgg
    tgggtatgagtgagaggttctcactctattagttcctgagagagctggttgtcaaaaaga
    gcctggcatctccctcccccttgcttcttctctgccatgtgacctctacacaccctgcct
    tcccttcttccatgagttgaagcagtctgaggctctcaccagtgaagatgcccaattttg
    agctttccaaccatccagaaccataagccaaataaaactttttttttttttttaacaaat
    tactcagagtcaggtatttccttacagcaacacaaaatatgctagacagtgaggtgagtt
    aatgtaagtaaaacatggctgggcgtggtgactcacacctgtagtcccagcactttagga
    ggccaaggtgggcggatcacaaggtcaggagtttgagaccaccctggccaacatggtgaa
    acaccgtctgtgctaaaaacacacacaaaaaactagctgggtgtggtggcacacgcctgt
    agtcccagctactcgggaggttgagtcaggagaattgcttgaacccaggaggtggaggct
    gcagtgagccaagattgcgccactgcacttgagcctgggtaacagagcaagactctgtct
    agaaaaaaaaaatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg
    taacacatctgcaatcccagagagcagaggaattcatggttccatccccacctctctgga
    gaagcttgaggctctcgtggtctggggcatctggcatgaagtggatagtggagtcactag
    tatcatagtaggcaatgcccaagtatcctgaattccacagcacacacagatggatctgtc
    cagcaaggaagaaaggaaatcactattagaatcactcataagtgtagggtttaccatgtc

      [Part of this file has been deleted for brevity]

    gaaaccctgtctctactaaaaaatacaggccgggcacagtggctcacgcctgtaatccca
    gcactttgggaggccgaggcgggtggatcatgaggtcaagagatcgagactatcctggct
    aacatgatgaaaccccgtctctactaaaaatacaaaaaattagctgggcatggtggcggg
    cacctgtagtcccagctactcgggaggctgagtcaggagaatggtgtgaacccaggagac
    ggagcttgcagtgagctgaggtcgcaccactgcactccagcctgggtgatagagcgagac
    tctgtctcaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaattagccgggtgtggtggcag
    gcaacttaatcccagctacttgggaggcagaggcaggagaatcgtttgaacctgggaggc
    ggaggttgaagagaatagaagctctgctggtccagagaaggattgggccagggctctggg
    agaccagggagaaagagggcacatgtggtccctgttgactgtgagggtgggaatctgagg
    aaggctttggctcattgccccttgggtttgtccacagccatccttcccctgcggagtatg
    tcgaggtgctccaggagctacagcggctggagagtcgcctccagcccttcttgcagcgct
    actacgaggttctgggtgctgctgccaccacggactacaataacaatgtgagccctttga
    tggccctgccctttctcctcagccccagtactcccaaaacagaacaggctgaaatacaga
    taactctttccctccctggaaaaacattgcaacagggccaggtgcagtggctcacgcctg
    taatcccagcactttgggaggccaaggtgggcggatcatctgagatcgggagtttgagac
    cagcctggccaacatggtgcaaccccatctctactgaaaatataaacattagctggatgt
    agtggtgcacacctgtaatcccagctactcaggaggctgaggcaggagaatcgctagaac
    tcgggaggagggggttgcagtgagccgagattgcactactgcactctagcctgggtgaca
    gagcgagactgtctcaaaaaacaaaacaaaacaaaaaaacacacattgcaacaaaacaat
    ttctctctaaacctgtaagtgattttgtcctcccttacagagaaggtgataatctttgct
    gtaagcactgtcctcgtatcgtaccccttgtgcccctgaatgaatttagaaaatgtaaag
    tacaggagatcagtatatgatgacttactgattcatagtagtgttttaataggatgttcc
    ttatgtgaataagatataatttatttgcaaagatttggtctacatgtaaacttccaagga
    tataactgaaagttttggaggacatggtattctcagtaggcattattgcttttattagtg
    agatggactccagcttgatattttctgcctttttgtgtttggctggttgtgcgcagcacg
    agggccgggaggaggatcagcggttgatcaacttggtaggggagagcctgcgactgctgg
    gcaacacctttgttgcactgtctgacctgcgctgcaatctggcctgcacgcccccacgac
    acctgcatgtggtccggcctatgtctcactacaccacccccatggtgctccagcaggcag
    ccattcccatacaggtgggttagggggagtctggcctgagggagagtgaggggtgttgat
    agagtgacccagggtagctactgggcctgaaggaggttaggaaaggaggagactggaaac
    atggtgatgaaggctggagatactttagaggtttatcatgaggttttcttggttaggctc
    ttgtatttttctcacatctgcctgtccatctgtctttttcagatcaatgtgggaaccact
    gtgaccatgacaggaaatgggactcggccccccccaactcccaatgcagaggcacctccc
    cctggtcctgggcaggcctcatccgtggctccgtcttctaccaatgtcgagtcctcagct
    gagggggctcccccgccaggtccagctcccccgccagccaccagccacccgagggtcatc
    cggatttcccaccagagtgtggaacccgtggtcatgatgcacatgaacattcaaggtgag
    aatagttgctggcgagaagagcaggatcagcatgatgagggaggttcatgctgaggtgtg
    agggaacagggtggggaagggagaggcacatgctggtggtggtagcctggggaccagagc
    agaagcttaagtagacagatgtggggggtgtgggggttggtttgtctttggaggtgtgtt
    tgtgtggtgaagggagtacctctccctgtttagatggagggaaaggcaggctttctgatt
    gggggattatgggcctgaagtatgcctgatctcagaaggatatagttaggccttggccct
    acctacctcagggccactgtctctgtctccctgcccagattctggcacacagcctggtgg
    tgttccgagtgctcccactggccccctgggaccccctggtcatggccaaaccctgggtaa
    gagtgagggcatcagggcaggctgagctctgggtagagaaagggaagggctgagtgggtg
    ggttgaaggggtccaggttcaaggttacatcagacccgccccccaggctccaccctcatc
    cagctgccctccctgccccctgagttcatgcacgccgtcgcccaccagatcactcatcag
    gccatggtggcagctgttgcctccgcggccgcaggtaatgacctggaaggggaggcttgg
    gaggtagggcacagtccatggtggcagctggctggcaagggcctggccctcagccctctt
    cggtctgtctcttctgccacccacaggacagcaggtgccaggcttcccaacagctccaac
    ccgggtggtgattgcccggcccactcctccacaggctcggccttcccatcctggagggcc
    cccagtctctgggacactggtgagcaagggtcggggagttctagtgcgtaacagtctagg

The names of the sequences are the same as the original sequence, with '_start-end' appended, where 'start', and 'end' are the start and end positions of the sub-sequence. eg: The name HSHBB would be changed in the sub-sequences to: HSHBB_1-50000 and HSHBB_50001-73308 if they were split at the size of 50000 with no overlap.

## Data files

None.

## Notes

There should be little requirement to split sequences into smaller sub-sequences in EMBOSS, but there may be circumstances where memory usage becomes restrictive when dealing with truly large sequences.

## References

None

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

Bugs noted but not yet fixed. None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
skipseq | Reads and writes (returns) sequences, skipping the first few
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Completed 22 March 1999

## Target users

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

## Comments