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splitter |
Function
Split a sequence into (overlapping) smaller sequencesDescription
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 splitterSplit 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
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| 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 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
//
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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
NoneWarnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0Known bugs
None.See also
| 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 |
| 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 |
| 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