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splitsource |
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Split a sequence into original subsequences
% splitsource qasrswww:A01139 Split sequence(s) into original source sequences output sequence(s) [a01139.fasta]: |
Go to the input files for this example
Go to the output files for this example
Split sequence(s) into original source sequences
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-outseq] seqoutall [
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-outseq] (Parameter 2) |
seqoutall | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -feature | boolean | Retain feature information | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outseq" associated seqoutall qualifiers | ||||
| -osformat2 -osformat_outseq |
string | Output seq format | Any string | |
| -osextension2 -osextension_outseq |
string | File name extension | Any string | |
| -osname2 -osname_outseq |
string | Base file name | Any string | |
| -osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
| -osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
| -ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo2 -oufo_outseq |
string | UFO features | Any string | |
| -offormat2 -offormat_outseq |
string | Features format | Any string | |
| -ofname2 -ofname_outseq |
string | Features file name | Any string | |
| -ofdirectory2 -ofdirectory_outseq |
string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
ID A01139; SV 1; linear; unassigned DNA; PAT; PRO; 279 BP.
XX
AC A01139;
XX
DT 16-MAR-1994 (Rel. 38, Created)
DT 14-FEB-2001 (Rel. 66, Last updated, Version 5)
XX
DE Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin
DE coding sequence)
XX
KW .
XX
OS Lactococcus lactis
OC Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Lactococcus.
XX
OS Hirudo medicinalis (medicinal leech)
OC Eukaryota; Metazoa; Annelida; Clitellata; Hirudinida; Hirudinea;
OC Arhynchobdellida; Hirudiniformes; Hirudinidae; Hirudo.
XX
RN [1]
RP 1-279
RA Suri B., Schmitz A.;
RT "Bacterial vectors.";
RL Patent number EP0449770-A2/2, 02-OCT-1991.
RL CIBA-GEIGY AG.
XX
FH Key Location/Qualifiers
FH
FT source 1..81
FT /organism="Lactococcus lactis"
FT /focus
FT /strain="LM0230"
FT /mol_type="unassigned DNA"
FT /db_xref="taxon:1358"
FT source 82..279
FT /organism="Hirudo medicinalis"
FT /mol_type="unassigned DNA"
FT /db_xref="taxon:6421"
FT CDS 1..279
FT /transl_table=11
FT /note="fusion of MSP signal peptide and hirudin"
FT /protein_id="CAA00134.1"
FT /translation="MKKKIISAILMSTVILSAAAPLSGVYAVVYTDCTESGQNLCLCEG
FT SNVCGQGNKCILGSDGEKNQCVTGEGTPKPQSHNDGDFEEIPEEYLQ"
FT mat_peptide 82..279
FT /product="desulfatohirudin"
FT sig_peptide 1..81
FT /product="MSP signal peptide"
XX
SQ Sequence 279 BP; 76 A; 66 C; 68 G; 69 T; 0 other;
atgaaaaaaa agattatctc agctatttta atgtctacag tgatactttc tgctgcagcc 60
ccgttgtcag gtgtttacgc tgttgtttac accgactgca ccgaatctgg tcagaacctg 120
tgcctgtgcg aaggttctaa cgtttgcggt cagggtaaca aatgcatcct gggttctgac 180
ggtgaaaaaa accagtgcgt taccggcgaa ggtaccccga aaccgcagtc tcacaacgac 240
ggtgacttcg aagaaatccc ggaagaatac ctgcagtag 279
//
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The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
>A01139_1_1-81 organism="Lactococcus lactis" strain="LM0230" Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin coding sequence) atgaaaaaaaagattatctcagctattttaatgtctacagtgatactttctgctgcagcc ccgttgtcaggtgtttacgct >A01139_2_82-279 organism="Hirudo medicinalis" Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin coding sequence) gttgtttacaccgactgcaccgaatctggtcagaacctgtgcctgtgcgaaggttctaac gtttgcggtcagggtaacaaatgcatcctgggttctgacggtgaaaaaaaccagtgcgtt accggcgaaggtaccccgaaaccgcagtctcacaacgacggtgacttcgaagaaatcccg gaagaatacctgcagtag |
| Program name | Description |
|---|---|
| aligncopy | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Removes a section from a sequence |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieves sequence entries from flatfile databases and files |
| extractalign | Extract regions from a sequence alignment |
| extractfeat | Extract features from sequence(s) |
| extractseq | Extract regions from a sequence |
| featcopy | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| feattext | Return a feature table original text |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Create random nucleotide sequences |
| makeprotseq | Create random protein sequences |
| maskambignuc | Masks all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Masks all ambiguity characters in protein sequences with X |
| maskfeat | Write a sequence with masked features |
| maskseq | Write a sequence with masked regions |
| newseq | Create a sequence file from a typed-in sequence |
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
| noreturn | Remove carriage return from ASCII files |
| nospace | Remove whitespace from an ASCII text file |
| notab | Replace tabs with spaces in an ASCII text file |
| notseq | Write to file a subset of an input stream of sequences |
| nthseq | Write to file a single sequence from an input stream of sequences |
| nthseqset | Reads and writes (returns) one set of sequences from many |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqcount | Reads and counts sequences |
| seqret | Reads and writes (returns) sequences |
| seqretsetall | Reads and writes (returns) many sets of sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitter | Split sequence(s) into smaller sequences |
| trimest | Remove poly-A tails from nucleotide sequences |
| trimseq | Remove unwanted characters from start and end of sequence(s) |
| trimspace | Remove extra whitespace from an ASCII text file |
| union | Concatenate multiple sequences into a single sequence |
| vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.