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iep |
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iep calculates the isoelectric point of a protein from its amino acid composition assuming that no electrostatic interactions change the propensity for ionization. Optionally, iep will plot the ionization curve with respect to pH and write an output file of the data, where for each pH point the number of bound electrons and charge is given.
For peptide fragments it is possible to exclude the charges of the amino and carboxy terminal residues.
% iep tsw:laci_ecoli Calculate the isoelectric point of proteins Output file [laci_ecoli.iep]: |
Go to the input files for this example
Go to the output files for this example
Example 2
% iep tsw:ifna2_human -disulphide 2 -lysinemodified 2 Calculate the isoelectric point of proteins Output file [ifna2_human.iep]: |
Go to the input files for this example
Go to the output files for this example
Calculate the isoelectric point of proteins
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
* -outfile outfile [*.iep] Output file name
Additional (Optional) qualifiers:
-amino integer [1] Number of N-termini (Integer 0 or more)
-carboxyl integer [1] Number of C-termini (Integer 0 or more)
-[no]termini boolean [Y] Include charge at N and C terminus
-lysinemodified integer [0] Number of modified lysines (Integer 0 or
more)
-disulphides integer [0] Number of disulphide bridges (Integer 0
or more)
Advanced (Unprompted) qualifiers:
-step float [.5] Step value for pH (Number from 0.010 to
1.000)
-plot toggle [N] Plot charge vs pH
-[no]report toggle [Y] Write results to a file
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
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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
-version boolean Report version number and exit
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
| -outfile | outfile | Output file name | Output file | <*>.iep |
| Additional (Optional) qualifiers | ||||
| -amino | integer | Number of N-termini | Integer 0 or more | 1 |
| -carboxyl | integer | Number of C-termini | Integer 0 or more | 1 |
| -[no]termini | boolean | Include charge at N and C terminus | Boolean value Yes/No | Yes |
| -lysinemodified | integer | Number of modified lysines | Integer 0 or more | 0 |
| -disulphides | integer | Number of disulphide bridges | Integer 0 or more | 0 |
| Advanced (Unprompted) qualifiers | ||||
| -step | float | Step value for pH | Number from 0.010 to 1.000 | .5 |
| -plot | toggle | Plot charge vs pH | Toggle value Yes/No | No |
| -[no]report | toggle | Write results to a file | Toggle value Yes/No | Yes |
| 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 | |
| "-graph" associated xygraph qualifiers | ||||
| -gprompt | boolean | Graph prompting | Boolean value Yes/No | N |
| -gdesc | string | Graph description | Any string | |
| -gtitle | string | Graph title | Any string | |
| -gsubtitle | string | Graph subtitle | Any string | |
| -gxtitle | string | Graph x axis title | Any string | |
| -gytitle | string | Graph y axis title | Any string | |
| -goutfile | string | Output file for non interactive displays | Any string | |
| -gdirectory | string | Output directory | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | 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 LACI_ECOLI Reviewed; 360 AA.
AC P03023; O09196; P71309; Q2MC79; Q47338;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2003, sequence version 3.
DT 15-JUN-2010, entry version 117.
DE RecName: Full=Lactose operon repressor;
GN Name=lacI; OrderedLocusNames=b0345, JW0336;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0;
RA Farabaugh P.J.;
RT "Sequence of the lacI gene.";
RL Nature 274:765-769(1978).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Chen J., Matthews K.K.S.M.;
RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Marsh S.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA Mau B., Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1474(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains
[Part of this file has been deleted for brevity]
FT CHAIN 1 360 Lactose operon repressor.
FT /FTId=PRO_0000107963.
FT DOMAIN 1 58 HTH lacI-type.
FT DNA_BIND 6 25 H-T-H motif.
FT VARIANT 282 282 Y -> D (in T41 mutant).
FT MUTAGEN 17 17 Y->H: Broadening of specificity.
FT MUTAGEN 22 22 R->N: Recognizes an operator variant.
FT CONFLICT 286 286 L -> S (in Ref. 1, 4 and 7).
FT HELIX 6 11
FT TURN 12 14
FT HELIX 17 24
FT HELIX 33 45
FT HELIX 51 56
FT STRAND 63 69
FT HELIX 74 89
FT STRAND 93 98
FT STRAND 101 103
FT HELIX 104 115
FT TURN 116 118
FT STRAND 122 126
FT HELIX 130 139
FT TURN 140 142
FT STRAND 145 150
FT STRAND 154 156
FT STRAND 158 161
FT HELIX 163 177
FT STRAND 181 186
FT HELIX 192 207
FT STRAND 213 217
FT HELIX 222 234
FT STRAND 240 246
FT HELIX 247 259
FT TURN 265 267
FT STRAND 268 271
FT HELIX 277 281
FT STRAND 282 284
FT STRAND 287 290
FT HELIX 293 308
FT STRAND 314 319
FT STRAND 322 324
FT STRAND 334 338
FT HELIX 343 353
FT HELIX 354 356
SQ SEQUENCE 360 AA; 38590 MW; 347A8DEE92D736CB CRC64;
MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ
SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS
GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ
QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT
AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPLTTIK QDFRLLGQTS
VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ
//
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ID IFNA2_HUMAN Reviewed; 188 AA.
AC P01563; P01564; Q14606; Q96KI6;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 23-MAR-2010, entry version 109.
DE RecName: Full=Interferon alpha-2;
DE Short=IFN-alpha-2;
DE AltName: Full=Interferon alpha-A;
DE Short=LeIF A;
DE Flags: Precursor;
GN Name=IFNA2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RX MEDLINE=81052322; PubMed=6159538; DOI=10.1038/287411a0;
RA Goeddel D.V., Yelverton E., Ullrich A., Heyneker H.L., Miozzari G.,
RA Holmes W., Seeburg P.H., Dull T.J., May L., Stebbing N., Crea R.,
RA Maeda S., McCandliss R., Sloma A., Tabor J.M., Gross M.,
RA Familletti P.C., Pestka S.;
RT "Human leukocyte interferon produced by E. coli is biologically
RT active.";
RL Nature 287:411-416(1980).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RX MEDLINE=81148795; PubMed=6163083; DOI=10.1038/290020a0;
RA Goeddel D.V., Leung D.W., Dull T.J., Gross M., Lawn R.M.,
RA McCandliss R., Seeburg P.H., Ullrich A., Yelverton E., Gray P.W.;
RT "The structure of eight distinct cloned human leukocyte interferon
RT cDNAs.";
RL Nature 290:20-26(1981).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RX MEDLINE=82060261; PubMed=6170983; DOI=10.1073/pnas.78.9.5435;
RA Lawn R.M., Gross M., Houck C.M., Franke A.E., Gray P.V., Goeddel D.V.;
RT "DNA sequence of a major human leukocyte interferon gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 78:5435-5439(1981).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Bone marrow tumor;
RX MEDLINE=86069501; PubMed=3906813;
RA Oliver G., Balbas P., Valle F., Soberon X., Bolivar F.;
RT "Cloning of human leukocyte interferon cDNA and a strategy for its
RT production in E. coli.";
RL Rev. Latinoam. Microbiol. 27:141-150(1985).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[Part of this file has been deleted for brevity]
DR GO; GO:0006917; P:induction of apoptosis; TAS:ProtInc.
DR GO; GO:0006954; P:inflammatory response; TAS:ProtInc.
DR GO; GO:0009615; P:response to virus; IEA:UniProtKB-KW.
DR InterPro; IPR009079; 4_helix_cytokine-like_core.
DR InterPro; IPR000471; IInterferon_alpha/beta/delta.
DR InterPro; IPR015589; Interferon_alpha.
DR PANTHER; PTHR11691:SF9; IFNa; 1.
DR PANTHER; PTHR11691; Interferon_abd; 1.
DR Pfam; PF00143; Interferon; 1.
DR PRINTS; PR00266; INTERFERONAB.
DR SMART; SM00076; IFabd; 1.
DR SUPFAM; SSF47266; 4_helix_cytokine; 1.
DR PROSITE; PS00252; INTERFERON_A_B_D; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Complete proteome; Cytokine;
KW Direct protein sequencing; Disulfide bond; Glycoprotein;
KW Pharmaceutical; Polymorphism; Secreted; Signal.
FT SIGNAL 1 23
FT CHAIN 24 188 Interferon alpha-2.
FT /FTId=PRO_0000016360.
FT CARBOHYD 129 129 O-linked (GalNAc...).
FT /FTId=CAR_000049.
FT DISULFID 24 121
FT DISULFID 52 161
FT VARIANT 6 6 A -> D (in dbSNP:rs35971916).
FT /FTId=VAR_055972.
FT VARIANT 46 46 K -> R (in alpha-2B and alpha-2C;
FT dbSNP:rs1061959).
FT /FTId=VAR_004012.
FT VARIANT 57 57 H -> R (in alpha-2C).
FT /FTId=VAR_013001.
FT VARIANT 177 177 S -> L (in a breast cancer sample;
FT somatic mutation).
FT /FTId=VAR_036329.
FT HELIX 33 44
FT TURN 49 54
FT HELIX 63 66
FT STRAND 67 69
FT STRAND 71 75
FT HELIX 76 91
FT HELIX 93 98
FT HELIX 101 123
FT HELIX 134 155
FT HELIX 160 178
FT TURN 179 182
SQ SEQUENCE 188 AA; 21550 MW; 101DD21D394CBF97 CRC64;
MALTFALLVA LLVLSCKSSC SVGCDLPQTH SLGSRRTLML LAQMRKISLF SCLKDRHDFG
FPQEEFGNQF QKAETIPVLH EMIQQIFNLF STKDSSAAWD ETLLDKFYTE LYQQLNDLEA
CVIQGVGVTE TPLMKEDSIL AVRKYFQRIT LYLKEKKYSP CAWEVVRAEI MRSFSLSTNL
QESLRSKE
//
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The output is to the specified graphics device.
The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.
The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.
IEP of LACI_ECOLI from 1 to 360 Isoelectric Point = 6.8820 pH Bound Charge 1.00 81.96 37.96 1.50 81.89 37.89 2.00 81.65 37.65 2.50 80.91 36.91 3.00 78.79 34.79 3.50 73.70 29.70 4.00 65.15 21.15 4.50 56.73 12.73 5.00 51.75 7.75 5.50 49.36 5.36 6.00 47.63 3.63 6.50 45.56 1.56 7.00 43.59 -0.41 7.50 42.27 -1.73 8.00 41.22 -2.78 8.50 39.87 -4.13 9.00 38.26 -5.74 9.50 36.24 -7.76 10.00 33.03 -10.97 10.50 28.46 -15.54 11.00 23.58 -20.42 11.50 19.41 -24.59 12.00 15.19 -28.81 12.50 9.75 -34.25 13.00 4.64 -39.36 13.50 1.75 -42.25 14.00 0.59 -43.41 |
IEP of IFNA2_HUMAN from 1 to 188 Isoelectric Point = 5.7322 pH Bound Charge 1.00 52.98 22.98 1.50 52.93 22.93 2.00 52.77 22.77 2.50 52.28 22.28 3.00 50.87 20.87 3.50 47.47 17.47 4.00 41.62 11.62 4.50 35.67 5.67 5.00 32.10 2.10 5.50 30.47 0.47 6.00 29.51 -0.49 6.50 28.55 -1.45 7.00 27.65 -2.35 7.50 27.01 -2.99 8.00 26.36 -3.64 8.50 25.41 -4.59 9.00 24.25 -5.75 9.50 22.81 -7.19 10.00 20.49 -9.51 10.50 17.03 -12.97 11.00 13.16 -16.84 11.50 10.04 -19.96 12.00 7.49 -22.51 12.50 4.72 -25.28 13.00 2.23 -27.77 13.50 0.84 -29.16 14.00 0.28 -29.72 |
For each pH point it gives the number of bound electrons and the charge.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Here is the default Epk.dat file:
# pK values for amino acids # O=Ornithine J=Hydroxyproline # # Amino acid pK Amino 8.6 Carboxyl 3.6 C 8.5 D 3.9 E 4.1 H 6.5 K 10.8 R 12.5 Y 10.1
Adjusting the pH of an aqueous protein solution to the point where the numbers of positive and negative charges on the protein are equal brings the protein to its isoelectric point. This is often the point of lowest solubility, presumably because it is the point at which there are fewest intermolecular repulsions, so that the molecules tend to form aggregates.
Modified lysines and disulphide bridges affect the contributions of those residues to the protein charge. A set number of each residue can be excluded.
| Program name | Description |
|---|---|
| abiview | Display the trace in an ABI sequencer file |
| charge | Draw a protein charge plot |
| cirdna | Draws circular maps of DNA constructs |
| hmoment | Calculate and plot hydrophobic moment for protein sequence(s) |
| lindna | Draws linear maps of DNA constructs |
| octanol | Draw a White-Wimley protein hydropathy plot |
| pepinfo | Plot amino acid properties of a protein sequence in parallel |
| pepnet | Draw a helical net for a protein sequence |
| pepstats | Calculates statistics of protein properties |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| pepwindow | Draw a hydropathy plot for a protein sequence |
| pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| prettyplot | Draw a sequence alignment with pretty formatting |
| prettyseq | Write a nucleotide sequence and its translation to file |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| showfeat | Display features of a sequence in pretty format |
| showpep | Displays protein sequences with features in pretty format |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.