
                                 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

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

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

   Advanced (Unprompted) qualifiers:
   -addoverlap         boolean    Add overlap to size

   Associated qualifiers:

   "-sequence" 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

   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
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outseq]
   (Parameter 2) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Additional (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 (Unprompted) 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     9708
0
     ctactaaaaa tacaaaaaat tagctgggca tggtggcggg cacctgtagt cccagctact     9714
0
     cgggaggctg agtcaggaga atggtgtgaa cccaggagac ggagcttgca gtgagctgag     9720
0
     gtcgcaccac tgcactccag cctgggtgat agagcgagac tctgtctcaa aaaaaaaaaa     9726
0
     aaaaaaaaaa aaaacaaaaa ttagccgggt gtggtggcag gcaacttaat cccagctact     9732
0
     tgggaggcag aggcaggaga atcgtttgaa cctgggaggc ggaggttgaa gagaatagaa     9738
0
     gctctgctgg tccagagaag gattgggcca gggctctggg agaccaggga gaaagagggc     9744
0
     acatgtggtc cctgttgact gtgagggtgg gaatctgagg aaggctttgg ctcattgccc     9750
0
     cttgggtttg tccacagcca tccttcccct gcggagtatg tcgaggtgct ccaggagcta     9756
0
     cagcggctgg agagtcgcct ccagcccttc ttgcagcgct actacgaggt tctgggtgct     9762
0
     gctgccacca cggactacaa taacaatgtg agccctttga tggccctgcc ctttctcctc     9768
0
     agccccagta ctcccaaaac agaacaggct gaaatacaga taactctttc cctccctgga     9774
0
     aaaacattgc aacagggcca ggtgcagtgg ctcacgcctg taatcccagc actttgggag     9780
0
     gccaaggtgg gcggatcatc tgagatcggg agtttgagac cagcctggcc aacatggtgc     9786
0
     aaccccatct ctactgaaaa tataaacatt agctggatgt agtggtgcac acctgtaatc     9792
0
     ccagctactc aggaggctga ggcaggagaa tcgctagaac tcgggaggag ggggttgcag     9798
0
     tgagccgaga ttgcactact gcactctagc ctgggtgaca gagcgagact gtctcaaaaa     9804
0
     acaaaacaaa acaaaaaaac acacattgca acaaaacaat ttctctctaa acctgtaagt     9810
0
     gattttgtcc tcccttacag agaaggtgat aatctttgct gtaagcactg tcctcgtatc     9816
0
     gtaccccttg tgcccctgaa tgaatttaga aaatgtaaag tacaggagat cagtatatga     9822
0
     tgacttactg attcatagta gtgttttaat aggatgttcc ttatgtgaat aagatataat     9828
0
     ttatttgcaa agatttggtc tacatgtaaa cttccaagga tataactgaa agttttggag     9834
0
     gacatggtat tctcagtagg cattattgct tttattagtg agatggactc cagcttgata     9840
0
     ttttctgcct ttttgtgttt ggctggttgt gcgcagcacg agggccggga ggaggatcag     9846
0
     cggttgatca acttggtagg ggagagcctg cgactgctgg gcaacacctt tgttgcactg     9852
0
     tctgacctgc gctgcaatct ggcctgcacg cccccacgac acctgcatgt ggtccggcct     9858
0
     atgtctcact acaccacccc catggtgctc cagcaggcag ccattcccat acaggtgggt     9864
0
     tagggggagt ctggcctgag ggagagtgag gggtgttgat agagtgaccc agggtagcta     9870
0
     ctgggcctga aggaggttag gaaaggagga gactggaaac atggtgatga aggctggaga     9876
0
     tactttagag gtttatcatg aggttttctt ggttaggctc ttgtattttt ctcacatctg     9882
0
     cctgtccatc tgtctttttc agatcaatgt gggaaccact gtgaccatga caggaaatgg     9888
0
     gactcggccc cccccaactc ccaatgcaga ggcacctccc cctggtcctg ggcaggcctc     9894
0
     atccgtggct ccgtcttcta ccaatgtcga gtcctcagct gagggggctc ccccgccagg     9900
0
     tccagctccc ccgccagcca ccagccaccc gagggtcatc cggatttccc accagagtgt     9906
0
     ggaacccgtg gtcatgatgc acatgaacat tcaaggtgag aatagttgct ggcgagaaga     9912
0
     gcaggatcag catgatgagg gaggttcatg ctgaggtgtg agggaacagg gtggggaagg     9918
0
     gagaggcaca tgctggtggt ggtagcctgg ggaccagagc agaagcttaa gtagacagat     9924
0
     gtggggggtg tgggggttgg tttgtctttg gaggtgtgtt tgtgtggtga agggagtacc     9930
0
     tctccctgtt tagatggagg gaaaggcagg ctttctgatt gggggattat gggcctgaag     9936
0
     tatgcctgat ctcagaagga tatagttagg ccttggccct acctacctca gggccactgt     9942
0
     ctctgtctcc ctgcccagat tctggcacac agcctggtgg tgttccgagt gctcccactg     9948
0
     gccccctggg accccctggt catggccaaa ccctgggtaa gagtgagggc atcagggcag     9954
0
     gctgagctct gggtagagaa agggaagggc tgagtgggtg ggttgaaggg gtccaggttc     9960
0
     aaggttacat cagacccgcc ccccaggctc caccctcatc cagctgccct ccctgccccc     9966
0
     tgagttcatg cacgccgtcg cccaccagat cactcatcag gccatggtgg cagctgttgc     9972
0
     ctccgcggcc gcaggtaatg acctggaagg ggaggcttgg gaggtagggc acagtccatg     9978
0
     gtggcagctg gctggcaagg gcctggccct cagccctctt cggtctgtct cttctgccac     9984
0
     ccacaggaca gcaggtgcca ggcttcccaa cagctccaac ccgggtggtg attgcccggc     9990
0
     ccactcctcc acaggctcgg ccttcccatc ctggagggcc cccagtctct gggacactgg     9996
0
     tgagcaaggg tcggggagtt ctagtgcgta acagtctagg                          10000
0
//

Output File Format

  Output files for usage example

  File: ap000504.split

>AP000504_1-10000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I regi
on, 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 regi
on, 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

   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 © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   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

   None
