|   | splitter | 
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'.
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
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-outseq]            seqoutall  [ | 
| 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 | 
| 
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
//
 | 
| >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 | 
| >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.
| Program name | Description | 
|---|---|
| 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 |