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:BA000025 ba000025.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:BA000025 ba000025.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(s) filename and optional format, or
                                  reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers:
   -size               integer    [10000] Size to split at (Integer 1 or more)
   -overlap            integer    [0] Overlap between split sequences (Integer
                                  0 or more)
   -source             boolean    [N] Split using source features with /origid
                                  qualifiers
   -multifile          boolean    [N] Split sequence into multiple files

   Advanced (Unprompted) qualifiers:
   -feature            boolean    [N] Use feature information
   -addoverlap         boolean    [N] 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 dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)		 Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-outseq]
(Parameter 2)		 Sequence set(s) filename and optional format (output USA) Writeable sequence(s) <*>.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
-source Split using source features with /origid qualifiers Boolean value Yes/No No
-multifile Split sequence into multiple files Boolean value Yes/No No
Advanced (Unprompted) qualifiers Allowed values Default
-feature Use feature information Boolean value Yes/No No
-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:BA000025' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:BA000025

ID   BA000025; SV 2; linear; genomic DNA; STD; HUM; 2229817 BP.
XX
AC   BA000025; AP000502-AP000521;
XX
DT   09-DEC-2004 (Rel. 82, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 4)
XX
DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-2229817
RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
RT   ;
RL   Submitted (21-AUG-2001) 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   EPD; EP11158; HS_TNF.
DR   EPD; EP11159; HS_LTA.
DR   EPD; EP73522; HS_HLA-B.
DR   EPD; EP73908; HS_GTF2H4.
DR   EPD; EP73940; HS_NEU1.
DR   EPD; EP74013; HS_VARS2.
DR   EPD; EP74203; HS_MRPS18B.
DR   EPD; EP74346; HS_HLA-E.
DR   EPD; EP74389; HS_BAT1.
DR   EPD; EP74485; HS_IER3.
DR   GDB; 11515913.
DR   GOA; P59942.
DR   IMGT/HLA; HLA02629; J*01010102.
DR   RFAM; RF00017.
DR   RFAM; RF00019.
DR   RFAM; RF00026.
DR   RFAM; RF00100.
DR   RFAM; RF00137.
DR   RFAM; RF00276.


  [Part of this file has been deleted for brevity]

     ttggccccac cccagcatgt ctccaggttc ctctcagccc tggttccttt tggccctgca   2226900
     gtcacaatgg gcaacactgt gacgcaccct gtcctgtgtc acagtgtcat acactcaggc   2226960
     tcacattgcc cctaggccac ttgccagcca agggacatgg ccacattttg tgtcttctgc   2227020
     acctcagcct tgctttcaag tgcaggtgat gatggcaccc acgcagaaca aatgttattt   2227080
     gctatcttcg tcgagtttag tcatccaatt ttccaaccct cactgggcaa ggaagagtgt   2227140
     ggtttccacc aagaaggcag gatgtcagca gtcacagggg caaccaacag ggaaagccgc   2227200
     cggaaaatag accccacagg aagcacaggt gtccagtgga gatgggaacc ctgcagattt   2227260
     gaccgtcttt aagcagatta gagagattac cgttactaac aacttagcca taaaagttta   2227320
     ttagctattt tcaaaaagca taaaattatg taatataatt ttttttaaat ttccatcaat   2227380
     acaaaactaa tctgggcact gcaacttccg gtgggcaact gggataggcg gcatcatcag   2227440
     gaaggcgagc cctgccgtgc cccatgtgcc agtgccccag atggcggcag cctccccaga   2227500
     agcaccttgt atctcccctg cacagggcca gggtcccagc ttcccataca ccttctcctg   2227560
     ctttttcttt tctgtccttt cctttttcaa taaaccacct gcaaaaaggg aaaaccattc   2227620
     tgaggacaag aaacatgtca atgggaaata cacagttgcc agagggtaaa aggccctgtt   2227680
     cattctcatt gaaaagctca ggtatttctg ttaaagtctc tccttttact ttaggatgct   2227740
     gactcctgcg tccatctcaa cctgggcatc gtgccaccac cttcaagaag agaaaaacta   2227800
     agtagtgctt tgcaaagggg cagcagcatt tctcatttct gaccatgtca ggcacatggc   2227860
     catgcagatg agcaggtggg ggacacaggt gagtctccag acctgctctc ctcccacagt   2227920
     acattcttga gtctttttaa acagttgtga aaatgccaca gatgcaagca cctgtgggcc   2227980
     actcccatgg ggaccgttgc acaaggcagt gccactcatt ctcagaacct cctaccatgg   2228040
     gctatgctta gtgacccgag gccaagccaa ggaagacgcc agccacaggg tgccatcctc   2228100
     aggggcatgc tgccagcagg ggcaaagtta tccctagcaa caagatacag aaagaaagaa   2228160
     aaaaggaagg aaatgtagcc aatgggccgg ttcaggttct tgactttgcc acacaaaaga   2228220
     atttgagagc aagtccaaag taaaagtcag caagagaatt tattgcaaag tgaaagtaca   2228280
     ctctgacagc tgatcagagc agctgctcaa aagagagaca gtaccctccc ctcacgggag   2228340
     tcttacatga ttattcatga ataggtggga aggggtattg ttttaagcat gttctgtggt   2228400
     ctcttgaacg tgcatgcact gtggttgtac atatcagcac acacatctta cgtctcatta   2228460
     gcatcttaac ttccctctca gagttgtgtt tgctactatt gtaatgagca taggtcagcc   2228520
     caaggacact attcatgggt ttctgggctt cctcagatgt ggggatgcct cccttggctc   2228580
     ttctacctct ttgctgcagg atgttctaac cacaagccca ggatatggtt tgcgcactgt   2228640
     cgaacagctt gttctctcca tcaacctgac aagtctcttg tttcctttca agggaggctg   2228700
     tgaacaccct atctcactga cctcagaagg acagtacagc agtagccacc atgaccaaaa   2228760
     agatgattcc agaagtgcag gacaactccc tacccagagg ctgtggctgt gcagtaacac   2228820
     accaagaggg gagtccagct ggctctcagg gtgctcacta ccctcatctg ggggcctgga   2228880
     ggacgtcaat tcctgagaac gccacgttct agtgagtaga atgaactgag agatacacag   2228940
     caaagctcca catacttttc cttttctttg tgcccgcagt gttcttcatc agtgtgctct   2229000
     cgcttttcag ctactactgt tggctggctg gaaaaaatag aacaatagta aaaattagag   2229060
     accagtcttt ggtgatgaag agaaatattg gctacttcca gtattttcta gctttggtta   2229120
     tggttgcagt tttccagctc accttgtggg gatgaattca gaaaaaagtt acaaattgaa   2229180
     atgaacatgc cagaagtatt ggctcaaatc aacgttgtcc tattaagcca cttagtgaat   2229240
     caaaagaccg cttgttggac tgttaatctc ggtggccaga gaaaggagct gaagaaggtg   2229300
     ttgccagatc aggaacaaat aattacagcg gcaatagaaa atggaagacc acttgttcat   2229360
     aaccatttga ataagggcaa ggtgtatgga aacacattat gaactgatat tttcagtttt   2229420
     gtttgcaaga aaatgattaa taaggtgaaa taattgaagt atcacggaag atacattaaa   2229480
     aaaaaaaaaa gcctttgtac agtttgctgg agccacagat gtcctactcc agagcagaac   2229540
     aatgcctgaa tcttcagggt ccatttctgc cgcattcact agcaaccaca aatgtgactt   2229600
     aattttactt tggaaataat gcttacccat tgtgagatgc tgtaatatga accatcatta   2229660
     catgttaaca tggcacatgg aattttgagt gtctaagtta catttttaga gttgtttctt   2229720
     agtagccatg tgagtttcca ctccaaaaac acaagctaaa aacttgtttt gagtgaagga   2229780
     catctagggc aaatggtggc tgaaagtgaa tgagatc                            2229817
//

Output File Format

Output files for usage example

File: ba000025.split

>BA000025_1-10000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
gatctccagagcactcttccctgcagggcaccctcccatcccagactccaggcacctggc
atgggtggacatctttactttctgggccagcttcagcagagctatgtcatcaccatagaa
ctccaggattccctggttctttttggcaaagacatcaaaccctggggagatcaccgcctt
ctcaataaggaattctttgccccactgggatttggggtctcctggaaatgatacactaga
ttaggctagaccagggctcctgcaggggccagaggctgggtgaggtggtaggatctgtgg
cttcaggatcaggaggctggtgcatcccctgccttacccacattgaccctccacagggag
tggtcgttgccatcgcggaagcaatgagctgctgtcaggacccattggtcggagatgagg
gccccccggcaggtctcttggctcttgggctgcaggggaacaggtgattttcagagattg
cagtatgtctggcccatggccgcttttacctctggaatccaagccctgcccctccttcct
ggtaccttaatagtgacatgccagggtgtcctctcctggtcagaggcgtttgctgacatg
ttccccaccccgcagatggtgtctgtgagcttggagacatctgtgggtgtgaggatcaga
tggggaaggaggcaagtgaggggcactgtgtccaggttcccaacacgggcctctggcggg
ctcctcaccatcctccccacaccaaggagggcaaagctcactcacccagcatatgttcaa
agacctggtgcagagcctttgtgtcctgcagaatgaaggcatgcctctcaccatccttct
tggaccctagctcattcagttctctccagtccacatccagcttgcccaccccgatggcat
agatgtctggtggggaagagggaaatcaccagactcctgtggctttggggctaccccatg
agacaggaggctgtcatctgaaactcactgtgtccaatcaagacctacatgagctggacc
cctgcgtcctccccactgctacctgtctgccttcatttcctgccactccctgcccttcac
tctcctgcagcacacagcctctttgaagttcctcaaatccataggcatggtcacacctca
ggccctttgcccagctgtgcctctgcctagttcactcctcccccccagacttccacatgg
ctcactttcgtacctttttaagtcttggctcaaatgtcaccttctcagtgaggccttccc
tggtcttcctgtctaaaactgcaatgccccagacaaactttcatccccactttgggaggc
aaggtgggaggatcccttgaagccagaagtttgagaccagcctgggcaacatggcaacac
cccttagcttgtgtcacctaccacctgctgggttctatggttttcttatcctgtttattc
cctgtaatggtggaattgtgtcccccagaaagatgtgttcgagtcctaatccccagtatc
tgtgactttatttggaaaaagggtctttgcagatgtaatcaagttaagattaagtcatac
tagattagggtgagctctaatccaatgactgaggtccttataagaagaggtaagccagag
ccaggcgtggtggctcacacctgtaatcaccaggaggcggtggttgtggtgagccaagat
cgcgccattgcactccagcctgggcaacaagagcaaaaccccgtctcaaaaaaaaaaaaa
gaagaggtgagccgggcacggtggctcacacctgtaatcccagcactctgggaggctgag
gcgggcagatcacgaggtcaggaattcaagaccagcctgaccaacatggtgaaaccctgt
ctctactaaaaatacaaaaattagccagacatgctggcacacacctgtaatcccagctac
tcaggaggctgaggcaggagaatcgcttgaaccgggaggcggatgttgcagtgagccgag
attgcaccactgcactccagcctgggcaacagagcaagactccatctcaaaaaaaaaaaa
aaaaaaaaaaagtgaactggctgggcatggtggtgactcatgcctgtaatcccggcagtt
tttttgaggcgaaggcaggcagatcgccttgaggccaggagtttaagaccagcctagcca
acatggcgagaccatgtctctactaaaaatacaaaaatttgccgggcatggtggcacatg
cctgtaatcccagcttcttgggagactgaggcacgagaatcacctgaacccaggaggcag
aggttacagtgagccgggatcccgccactgcactgcagcctgggcttctgggtgacagag
cgagactctgtctcaaacaaatgaacagaaaaagaagaaaggaatttggacacaaagaca
caggtagtgggtctcctatctatataagagaacagcatgtaatgacacagaggcacacac
agaaaagaaggcgagttgaagacagaggcagagaatgggtttatgctgccgcaagccaag
gttggagctgccggcagccggaaaaggcaggaaagaattcttcccaagagccttctgagg
aagcacggccctgccaacaccttgatttcagacttctaacctccagaactgtaagaaaaa
gaaattctgtgttctaagccacccaggtttgtggtagtttggtaagtacttttaaatgac
tgaatgaatagaaagaactcagaacacaacatggaaactaaacctcagatctggtcttcc
tctgtaaaaggtagcatctgggagaagggcctaaagccacgttttcccactggaggccct
ggacccacacaacaggccgcgcctgtcctccgactgtggtgccagtcagaactgccctca
gacagaccacagagtctactcctctcccagcctttgcaccccttgtggcccatttttgtt


  [Part of this file has been deleted for brevity]

cctcggtctgtctccaccaggccctgtgagggtgggtggaggctctctccaagccctcgt
ttggccccaccccagcatgtctccaggttcctctcagccctggttccttttggccctgca
gtcacaatgggcaacactgtgacgcaccctgtcctgtgtcacagtgtcatacactcaggc
tcacattgcccctaggccacttgccagccaagggacatggccacattttgtgtcttctgc
acctcagccttgctttcaagtgcaggtgatgatggcacccacgcagaacaaatgttattt
gctatcttcgtcgagtttagtcatccaattttccaaccctcactgggcaaggaagagtgt
ggtttccaccaagaaggcaggatgtcagcagtcacaggggcaaccaacagggaaagccgc
cggaaaatagaccccacaggaagcacaggtgtccagtggagatgggaaccctgcagattt
gaccgtctttaagcagattagagagattaccgttactaacaacttagccataaaagttta
ttagctattttcaaaaagcataaaattatgtaatataattttttttaaatttccatcaat
acaaaactaatctgggcactgcaacttccggtgggcaactgggataggcggcatcatcag
gaaggcgagccctgccgtgccccatgtgccagtgccccagatggcggcagcctccccaga
agcaccttgtatctcccctgcacagggccagggtcccagcttcccatacaccttctcctg
ctttttcttttctgtcctttcctttttcaataaaccacctgcaaaaagggaaaaccattc
tgaggacaagaaacatgtcaatgggaaatacacagttgccagagggtaaaaggccctgtt
cattctcattgaaaagctcaggtatttctgttaaagtctctccttttactttaggatgct
gactcctgcgtccatctcaacctgggcatcgtgccaccaccttcaagaagagaaaaacta
agtagtgctttgcaaaggggcagcagcatttctcatttctgaccatgtcaggcacatggc
catgcagatgagcaggtgggggacacaggtgagtctccagacctgctctcctcccacagt
acattcttgagtctttttaaacagttgtgaaaatgccacagatgcaagcacctgtgggcc
actcccatggggaccgttgcacaaggcagtgccactcattctcagaacctcctaccatgg
gctatgcttagtgacccgaggccaagccaaggaagacgccagccacagggtgccatcctc
aggggcatgctgccagcaggggcaaagttatccctagcaacaagatacagaaagaaagaa
aaaaggaaggaaatgtagccaatgggccggttcaggttcttgactttgccacacaaaaga
atttgagagcaagtccaaagtaaaagtcagcaagagaatttattgcaaagtgaaagtaca
ctctgacagctgatcagagcagctgctcaaaagagagacagtaccctcccctcacgggag
tcttacatgattattcatgaataggtgggaaggggtattgttttaagcatgttctgtggt
ctcttgaacgtgcatgcactgtggttgtacatatcagcacacacatcttacgtctcatta
gcatcttaacttccctctcagagttgtgtttgctactattgtaatgagcataggtcagcc
caaggacactattcatgggtttctgggcttcctcagatgtggggatgcctcccttggctc
ttctacctctttgctgcaggatgttctaaccacaagcccaggatatggtttgcgcactgt
cgaacagcttgttctctccatcaacctgacaagtctcttgtttcctttcaagggaggctg
tgaacaccctatctcactgacctcagaaggacagtacagcagtagccaccatgaccaaaa
agatgattccagaagtgcaggacaactccctacccagaggctgtggctgtgcagtaacac
accaagaggggagtccagctggctctcagggtgctcactaccctcatctgggggcctgga
ggacgtcaattcctgagaacgccacgttctagtgagtagaatgaactgagagatacacag
caaagctccacatacttttccttttctttgtgcccgcagtgttcttcatcagtgtgctct
cgcttttcagctactactgttggctggctggaaaaaatagaacaatagtaaaaattagag
accagtctttggtgatgaagagaaatattggctacttccagtattttctagctttggtta
tggttgcagttttccagctcaccttgtggggatgaattcagaaaaaagttacaaattgaa
atgaacatgccagaagtattggctcaaatcaacgttgtcctattaagccacttagtgaat
caaaagaccgcttgttggactgttaatctcggtggccagagaaaggagctgaagaaggtg
ttgccagatcaggaacaaataattacagcggcaatagaaaatggaagaccacttgttcat
aaccatttgaataagggcaaggtgtatggaaacacattatgaactgatattttcagtttt
gtttgcaagaaaatgattaataaggtgaaataattgaagtatcacggaagatacattaaa
aaaaaaaaaagcctttgtacagtttgctggagccacagatgtcctactccagagcagaac
aatgcctgaatcttcagggtccatttctgccgcattcactagcaaccacaaatgtgactt
aattttactttggaaataatgcttacccattgtgagatgctgtaatatgaaccatcatta
catgttaacatggcacatggaattttgagtgtctaagttacatttttagagttgtttctt
agtagccatgtgagtttccactccaaaaacacaagctaaaaacttgttttgagtgaagga
catctagggcaaatggtggctgaaagtgaatgagatc

Output files for usage example 2

File: ba000025.split

>BA000025_1-50000 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region.
gatctccagagcactcttccctgcagggcaccctcccatcccagactccaggcacctggc
atgggtggacatctttactttctgggccagcttcagcagagctatgtcatcaccatagaa
ctccaggattccctggttctttttggcaaagacatcaaaccctggggagatcaccgcctt
ctcaataaggaattctttgccccactgggatttggggtctcctggaaatgatacactaga
ttaggctagaccagggctcctgcaggggccagaggctgggtgaggtggtaggatctgtgg
cttcaggatcaggaggctggtgcatcccctgccttacccacattgaccctccacagggag
tggtcgttgccatcgcggaagcaatgagctgctgtcaggacccattggtcggagatgagg
gccccccggcaggtctcttggctcttgggctgcaggggaacaggtgattttcagagattg
cagtatgtctggcccatggccgcttttacctctggaatccaagccctgcccctccttcct
ggtaccttaatagtgacatgccagggtgtcctctcctggtcagaggcgtttgctgacatg
ttccccaccccgcagatggtgtctgtgagcttggagacatctgtgggtgtgaggatcaga
tggggaaggaggcaagtgaggggcactgtgtccaggttcccaacacgggcctctggcggg
ctcctcaccatcctccccacaccaaggagggcaaagctcactcacccagcatatgttcaa
agacctggtgcagagcctttgtgtcctgcagaatgaaggcatgcctctcaccatccttct
tggaccctagctcattcagttctctccagtccacatccagcttgcccaccccgatggcat
agatgtctggtggggaagagggaaatcaccagactcctgtggctttggggctaccccatg
agacaggaggctgtcatctgaaactcactgtgtccaatcaagacctacatgagctggacc
cctgcgtcctccccactgctacctgtctgccttcatttcctgccactccctgcccttcac
tctcctgcagcacacagcctctttgaagttcctcaaatccataggcatggtcacacctca
ggccctttgcccagctgtgcctctgcctagttcactcctcccccccagacttccacatgg
ctcactttcgtacctttttaagtcttggctcaaatgtcaccttctcagtgaggccttccc
tggtcttcctgtctaaaactgcaatgccccagacaaactttcatccccactttgggaggc
aaggtgggaggatcccttgaagccagaagtttgagaccagcctgggcaacatggcaacac
cccttagcttgtgtcacctaccacctgctgggttctatggttttcttatcctgtttattc
cctgtaatggtggaattgtgtcccccagaaagatgtgttcgagtcctaatccccagtatc
tgtgactttatttggaaaaagggtctttgcagatgtaatcaagttaagattaagtcatac
tagattagggtgagctctaatccaatgactgaggtccttataagaagaggtaagccagag
ccaggcgtggtggctcacacctgtaatcaccaggaggcggtggttgtggtgagccaagat
cgcgccattgcactccagcctgggcaacaagagcaaaaccccgtctcaaaaaaaaaaaaa
gaagaggtgagccgggcacggtggctcacacctgtaatcccagcactctgggaggctgag
gcgggcagatcacgaggtcaggaattcaagaccagcctgaccaacatggtgaaaccctgt
ctctactaaaaatacaaaaattagccagacatgctggcacacacctgtaatcccagctac
tcaggaggctgaggcaggagaatcgcttgaaccgggaggcggatgttgcagtgagccgag
attgcaccactgcactccagcctgggcaacagagcaagactccatctcaaaaaaaaaaaa
aaaaaaaaaaagtgaactggctgggcatggtggtgactcatgcctgtaatcccggcagtt
tttttgaggcgaaggcaggcagatcgccttgaggccaggagtttaagaccagcctagcca
acatggcgagaccatgtctctactaaaaatacaaaaatttgccgggcatggtggcacatg
cctgtaatcccagcttcttgggagactgaggcacgagaatcacctgaacccaggaggcag
aggttacagtgagccgggatcccgccactgcactgcagcctgggcttctgggtgacagag
cgagactctgtctcaaacaaatgaacagaaaaagaagaaaggaatttggacacaaagaca
caggtagtgggtctcctatctatataagagaacagcatgtaatgacacagaggcacacac
agaaaagaaggcgagttgaagacagaggcagagaatgggtttatgctgccgcaagccaag
gttggagctgccggcagccggaaaaggcaggaaagaattcttcccaagagccttctgagg
aagcacggccctgccaacaccttgatttcagacttctaacctccagaactgtaagaaaaa
gaaattctgtgttctaagccacccaggtttgtggtagtttggtaagtacttttaaatgac
tgaatgaatagaaagaactcagaacacaacatggaaactaaacctcagatctggtcttcc
tctgtaaaaggtagcatctgggagaagggcctaaagccacgttttcccactggaggccct
ggacccacacaacaggccgcgcctgtcctccgactgtggtgccagtcagaactgccctca
gacagaccacagagtctactcctctcccagcctttgcaccccttgtggcccatttttgtt


  [Part of this file has been deleted for brevity]

ggagaggggcaggtgcccctcctcggtctgtctccaccaggccctgtgagggtgggtgga
ggctctctccaagccctcgtttggccccaccccagcatgtctccaggttcctctcagccc
tggttccttttggccctgcagtcacaatgggcaacactgtgacgcaccctgtcctgtgtc
acagtgtcatacactcaggctcacattgcccctaggccacttgccagccaagggacatgg
ccacattttgtgtcttctgcacctcagccttgctttcaagtgcaggtgatgatggcaccc
acgcagaacaaatgttatttgctatcttcgtcgagtttagtcatccaattttccaaccct
cactgggcaaggaagagtgtggtttccaccaagaaggcaggatgtcagcagtcacagggg
caaccaacagggaaagccgccggaaaatagaccccacaggaagcacaggtgtccagtgga
gatgggaaccctgcagatttgaccgtctttaagcagattagagagattaccgttactaac
aacttagccataaaagtttattagctattttcaaaaagcataaaattatgtaatataatt
ttttttaaatttccatcaatacaaaactaatctgggcactgcaacttccggtgggcaact
gggataggcggcatcatcaggaaggcgagccctgccgtgccccatgtgccagtgccccag
atggcggcagcctccccagaagcaccttgtatctcccctgcacagggccagggtcccagc
ttcccatacaccttctcctgctttttcttttctgtcctttcctttttcaataaaccacct
gcaaaaagggaaaaccattctgaggacaagaaacatgtcaatgggaaatacacagttgcc
agagggtaaaaggccctgttcattctcattgaaaagctcaggtatttctgttaaagtctc
tccttttactttaggatgctgactcctgcgtccatctcaacctgggcatcgtgccaccac
cttcaagaagagaaaaactaagtagtgctttgcaaaggggcagcagcatttctcatttct
gaccatgtcaggcacatggccatgcagatgagcaggtgggggacacaggtgagtctccag
acctgctctcctcccacagtacattcttgagtctttttaaacagttgtgaaaatgccaca
gatgcaagcacctgtgggccactcccatggggaccgttgcacaaggcagtgccactcatt
ctcagaacctcctaccatgggctatgcttagtgacccgaggccaagccaaggaagacgcc
agccacagggtgccatcctcaggggcatgctgccagcaggggcaaagttatccctagcaa
caagatacagaaagaaagaaaaaaggaaggaaatgtagccaatgggccggttcaggttct
tgactttgccacacaaaagaatttgagagcaagtccaaagtaaaagtcagcaagagaatt
tattgcaaagtgaaagtacactctgacagctgatcagagcagctgctcaaaagagagaca
gtaccctcccctcacgggagtcttacatgattattcatgaataggtgggaaggggtattg
ttttaagcatgttctgtggtctcttgaacgtgcatgcactgtggttgtacatatcagcac
acacatcttacgtctcattagcatcttaacttccctctcagagttgtgtttgctactatt
gtaatgagcataggtcagcccaaggacactattcatgggtttctgggcttcctcagatgt
ggggatgcctcccttggctcttctacctctttgctgcaggatgttctaaccacaagccca
ggatatggtttgcgcactgtcgaacagcttgttctctccatcaacctgacaagtctcttg
tttcctttcaagggaggctgtgaacaccctatctcactgacctcagaaggacagtacagc
agtagccaccatgaccaaaaagatgattccagaagtgcaggacaactccctacccagagg
ctgtggctgtgcagtaacacaccaagaggggagtccagctggctctcagggtgctcacta
ccctcatctgggggcctggaggacgtcaattcctgagaacgccacgttctagtgagtaga
atgaactgagagatacacagcaaagctccacatacttttccttttctttgtgcccgcagt
gttcttcatcagtgtgctctcgcttttcagctactactgttggctggctggaaaaaatag
aacaatagtaaaaattagagaccagtctttggtgatgaagagaaatattggctacttcca
gtattttctagctttggttatggttgcagttttccagctcaccttgtggggatgaattca
gaaaaaagttacaaattgaaatgaacatgccagaagtattggctcaaatcaacgttgtcc
tattaagccacttagtgaatcaaaagaccgcttgttggactgttaatctcggtggccaga
gaaaggagctgaagaaggtgttgccagatcaggaacaaataattacagcggcaatagaaa
atggaagaccacttgttcataaccatttgaataagggcaaggtgtatggaaacacattat
gaactgatattttcagttttgtttgcaagaaaatgattaataaggtgaaataattgaagt
atcacggaagatacattaaaaaaaaaaaaagcctttgtacagtttgctggagccacagat
gtcctactccagagcagaacaatgcctgaatcttcagggtccatttctgccgcattcact
agcaaccacaaatgtgacttaattttactttggaaataatgcttacccattgtgagatgc
tgtaatatgaaccatcattacatgttaacatggcacatggaattttgagtgtctaagtta
catttttagagttgtttcttagtagccatgtgagtttccactccaaaaacacaagctaaa
aacttgttttgagtgaaggacatctagggcaaatggtggctgaaagtgaatgagatc

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 nameDescription
biosed Replace or delete sequence sections
codcopy Reads and writes a codon usage table
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
extractalign Extract regions from a sequence alignment
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
listor Write a list file of the logical OR of two sets of sequences
makenucseq Creates random nucleotide sequences
makeprotseq Creates random protein 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 Exclude a set of sequences and write 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 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