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|
backtranseq
Function
Back translate a protein sequence
Description
backtranseq takes a protein sequence and makes a best estimate of the
likely nucleic acid sequence it could have come from. It does this by
using a codon frequency table. For each amino acid, the corresponding
most frequently occuring codon is used in the construction of the
nucleic acid sequence.
Codon usage table name
backtranseq reads in a data file containing the codon frequency
tables. The default codon frequency table is 'Ehum.cut' - the human
codon frequency table. It is important to use a codon frequency table
that is appropriate for the species that your protein comes from. See
the Data Files section below for more details on these files.
Usage
Here is a sample session with backtranseq
Note that this is a human protein and so the default human codon
frequency file is used ie. is not specified
% backtranseq
Back translate a protein sequence
Input (gapped) protein sequence: tsw:opsd_human
(gapped) nucleotide output sequence [opsd_human.fasta]:
Go to the input files for this example
Go to the output files for this example
Example 2
This uses a drosophila sequence and codon table.
% backtranseq -cfile Edrome.cut
Back translate a protein sequence
Input (gapped) protein sequence: tsw:ach2_drome
(gapped) nucleotide output sequence [ach2_drome.fasta]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] sequence (Gapped) protein sequence filename and
optional format, or reference (input USA)
[-outfile] seqout [.] (Gapped) nucleotide
sequence filename and optional format
(output USA)
Additional (Optional) qualifiers:
-cfile codon [Ehuman.cut] Codon usage table name
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
"-cfile" associated qualifiers
-format string Data format
"-outfile" 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
Input file format
Any DNA sequence USA.
Input files for usage example
'tsw:opsd_human' is a sequence entry in the example protein database
'tsw'
Database entry: tsw:opsd_human
ID OPSD_HUMAN Reviewed; 348 AA.
AC P08100; Q16414; Q2M249;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1988, sequence version 1.
DT 20-MAR-2007, entry version 91.
DE Rhodopsin (Opsin-2).
GN Name=RHO; Synonyms=OPN2;
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].
RX MEDLINE=84272729; PubMed=6589631;
RA Nathans J., Hogness D.S.;
RT "Isolation and nucleotide sequence of the gene encoding human
RT rhodopsin.";
RL Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT "Genome-wide discovery and analysis of human seven transmembrane helix
RT receptor genes.";
RL Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Retina;
RG The German cDNA consortium;
RL Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA Bennett J., Beller B., Sun D., Kariko K.;
RT "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT rhodopsin-encoding gene.";
RL Gene 167:317-320(1995).
RN [6]
RP REVIEW ON RP4 VARIANTS.
RX MEDLINE=94004905; PubMed=8401533;
RA Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA Bhattacharya S.;
[Part of this file has been deleted for brevity]
FT /FTId=VAR_004816.
FT VARIANT 209 209 V -> M (effect not known).
FT /FTId=VAR_004817.
FT VARIANT 211 211 H -> P (in RP4).
FT /FTId=VAR_004818.
FT VARIANT 211 211 H -> R (in RP4).
FT /FTId=VAR_004819.
FT VARIANT 216 216 M -> K (in RP4).
FT /FTId=VAR_004820.
FT VARIANT 220 220 F -> C (in RP4).
FT /FTId=VAR_004821.
FT VARIANT 222 222 C -> R (in RP4).
FT /FTId=VAR_004822.
FT VARIANT 255 255 Missing (in RP4).
FT /FTId=VAR_004823.
FT VARIANT 264 264 Missing (in RP4).
FT /FTId=VAR_004824.
FT VARIANT 267 267 P -> L (in RP4).
FT /FTId=VAR_004825.
FT VARIANT 267 267 P -> R (in RP4).
FT /FTId=VAR_004826.
FT VARIANT 292 292 A -> E (in CSNBAD1).
FT /FTId=VAR_004827.
FT VARIANT 296 296 K -> E (in RP4).
FT /FTId=VAR_004828.
FT VARIANT 297 297 S -> R (in RP4).
FT /FTId=VAR_004829.
FT VARIANT 342 342 T -> M (in RP4).
FT /FTId=VAR_004830.
FT VARIANT 345 345 V -> L (in RP4).
FT /FTId=VAR_004831.
FT VARIANT 345 345 V -> M (in RP4).
FT /FTId=VAR_004832.
FT VARIANT 347 347 P -> A (in RP4).
FT /FTId=VAR_004833.
FT VARIANT 347 347 P -> L (in RP4; common variant).
FT /FTId=VAR_004834.
FT VARIANT 347 347 P -> Q (in RP4).
FT /FTId=VAR_004835.
FT VARIANT 347 347 P -> R (in RP4).
FT /FTId=VAR_004836.
FT VARIANT 347 347 P -> S (in RP4).
FT /FTId=VAR_004837.
SQ SEQUENCE 348 AA; 38893 MW; 6F4F6FCBA34265B2 CRC64;
MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
Input files for usage example 2
Database entry: tsw:ach2_drome
ID ACH2_DROME Reviewed; 576 AA.
AC P17644; Q9VC73;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-APR-2007, entry version 78.
DE Acetylcholine receptor subunit alpha-like 2 precursor.
GN Name=nAcR-alpha-96Ab; Synonyms=Acr96Ab, AcrE, sad; ORFNames=CG6844;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC Ephydroidea; Drosophilidae; Drosophila.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Head;
RX MEDLINE=90301489; PubMed=2114015; DOI=10.1093/nar/18.12.3640;
RA Baumann A., Jonas P., Gundelfinger E.D.;
RT "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila
RT nicotinic acetylcholine receptors.";
RL Nucleic Acids Res. 18:3640-3640(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC TISSUE=Head;
RX MEDLINE=90353591; PubMed=2117557; DOI=10.1016/0014-5793(90)81170-S;
RA Jonas P., Baumann A., Merz B., Gundelfinger E.D.;
RT "Structure and developmental expression of the D alpha 2 gene encoding
RT a novel nicotinic acetylcholine receptor protein of Drosophila
RT melanogaster.";
RL FEBS Lett. 269:264-268(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX MEDLINE=90360975; PubMed=1697262;
RA Sawruk E., Schloss P., Betz H., Schmitt B.;
RT "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD, a
RT novel developmentally regulated alpha-subunit.";
RL EMBO J. 9:2671-2677(1990).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX MEDLINE=20196006; PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
RA Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
RA Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
RA Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
RA Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
RA Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
RA Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
[Part of this file has been deleted for brevity]
DR IntAct; P17644; -.
DR Ensembl; CG6844; Drosophila melanogaster.
DR KEGG; dme:Dmel_CG6844; -.
DR FlyBase; FBgn0000039; nAcR-alpha-96Ab.
DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013190-MONOMER; -.
DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013191-MONOMER; -.
DR GermOnline; CG6844; Drosophila melanogaster.
DR GO; GO:0005515; F:protein binding; IPI:IntAct.
DR InterPro; IPR006029; Neu_channel_TM.
DR InterPro; IPR006202; Neur_chan_lig_bd.
DR InterPro; IPR006201; Neur_channel.
DR InterPro; IPR002394; Nic_ach_rcpt.
DR Gene3D; G3DSA:3.30.1100.20; Neur_chan_lig_bd; 1.
DR PANTHER; PTHR18945; Neur_channel; 2.
DR Pfam; PF02931; Neur_chan_LBD; 1.
DR Pfam; PF02932; Neur_chan_memb; 1.
DR PRINTS; PR00254; NICOTINICR.
DR PRINTS; PR00252; NRIONCHANNEL.
DR TIGRFAMs; TIGR00860; LIC; 1.
DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
KW Complete proteome; Glycoprotein; Ion transport; Ionic channel;
KW Membrane; Postsynaptic membrane; Receptor; Signal; Transmembrane;
KW Transport.
FT SIGNAL 1 21 Probable.
FT CHAIN 22 576 Acetylcholine receptor subunit alpha-like
FT 2.
FT /FTId=PRO_0000000300.
FT TOPO_DOM 22 261 Extracellular (Potential).
FT TRANSMEM 262 285 Potential.
FT TRANSMEM 293 311 Potential.
FT TRANSMEM 327 346 Potential.
FT TOPO_DOM 347 526 Cytoplasmic (Potential).
FT TRANSMEM 527 545 Potential.
FT CARBOHYD 65 65 N-linked (GlcNAc...) (Potential).
FT CARBOHYD 254 254 N-linked (GlcNAc...) (Potential).
FT CARBOHYD 570 570 N-linked (GlcNAc...) (Potential).
FT DISULFID 169 183 By similarity.
FT DISULFID 243 244 Associated with receptor activation (By
FT similarity).
SQ SEQUENCE 576 AA; 65506 MW; 97D6A46CADC3F42F CRC64;
MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI
RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY
VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ
QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY
YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL
LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP
WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD
SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV
AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT
FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN
//
Output file format
The output is a nucleotide sequence containing the most favoured back
translation of the specified protein, and using the specified
translation table (which defaults to human).
Output files for usage example
File: opsd_human.fasta
>OPSD_HUMAN P08100 Rhodopsin (Opsin-2).
ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG
AGGAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG
GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC
GTGACCGTGCAGCACAAGAAGCTGAGGACCCCCCTGAACTACATCCTGCTGAACCTGGCC
GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC
GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC
GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGGTACGTGGTGGTGTGC
AAGCCCATGAGCAACTTCAGGTTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC
TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGGTACATCCCC
GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC
GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC
TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC
GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGGATGGTGATCATCATGGTGATCGCC
TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC
AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC
TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGGAACTGCATGCTGACCACC
ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC
GAGACCAGCCAGGTGGCCCCCGCC
Output files for usage example 2
File: ach2_drome.fasta
>ACH2_DROME P17644 Acetylcholine receptor subunit alpha-like 2 precursor.
ATGGCCCCCGGCTGCTGCACCACCCGCCCCCGCCCCATCGCCCTGCTGGCCCACATCTGG
CGCCACTGCAAGCCCCTGTGCCTGCTGCTGGTGCTGCTGCTGCTGTGCGAGACCGTGCAG
GCCAACCCCGATGCCAAGCGCCTGTACGATGATCTGCTGAGCAACTACAACCGCCTGATC
CGCCCCGTGAGCAACAACACCGATACCGTGCTGGTGAAGCTGGGCCTGCGCCTGAGCCAG
CTGATCGATCTGAACCTGAAGGATCAGATCCTGACCACCAACGTGTGGCTGGAGCACGAG
TGGCAGGATCACAAGTTCAAGTGGGATCCCAGCGAGTACGGCGGCGTGACCGAGCTGTAC
GTGCCCAGCGAGCACATCTGGCTGCCCGATATCGTGCTGTACAACAACGCCGATGGCGAG
TACGTGGTGACCACCATGACCAAGGCCATCCTGCACTACACCGGCAAGGTGGTGTGGACC
CCCCCCGCCATCTTCAAGAGCAGCTGCGAGATCGATGTGCGCTACTTCCCCTTCGATCAG
CAGACCTGCTTCATGAAGTTCGGCAGCTGGACCTACGATGGCGATCAGATCGATCTGAAG
CACATCAGCCAGAAGAACGATAAGGATAACAAGGTGGAGATCGGCATCGATCTGCGCGAG
TACTACCCCAGCGTGGAGTGGGATATCCTGGGCGTGCCCGCCGAGCGCCACGAGAAGTAC
TACCCCTGCTGCGCCGAGCCCTACCCCGATATCTTCTTCAACATCACCCTGCGCCGCAAG
ACCCTGTTCTACACCGTGAACCTGATCATCCCCTGCGTGGGCATCAGCTACCTGAGCGTG
CTGGTGTTCTACCTGCCCGCCGATAGCGGCGAGAAGATCGCCCTGTGCATCAGCATCCTG
CTGAGCCAGACCATGTTCTTCCTGCTGATCAGCGAGATCATCCCCAGCACCAGCCTGGCC
CTGCCCCTGCTGGGCAAGTACCTGCTGTTCACCATGCTGCTGGTGGGCCTGAGCGTGGTG
ATCACCATCATCATCCTGAACATCCACTACCGCAAGCCCAGCACCCACAAGATGCGCCCC
TGGATCCGCAGCTTCTTCATCAAGCGCCTGCCCAAGCTGCTGCTGATGCGCGTGCCCAAG
GATCTGCTGCGCGATCTGGCCGCCAACAAGATCAACTACGGCCTGAAGTTCAGCAAGACC
AAGTTCGGCCAGGCCCTGATGGATGAGATGCAGATGAACAGCGGCGGCAGCAGCCCCGAT
AGCCTGCGCCGCATGCAGGGCCGCGTGGGCGCCGGCGGCTGCAACGGCATGCACGTGACC
ACCGCCACCAACCGCTTCAGCGGCCTGGTGGGCGCCCTGGGCGGCGGCCTGAGCACCCTG
AGCGGCTACAACGGCCTGCCCAGCGTGCTGAGCGGCCTGGATGATAGCCTGAGCGATGTG
GCCGCCCGCAAGAAGTACCCCTTCGAGCTGGAGAAGGCCATCCACAACGTGATGTTCATC
CAGCACCACATGCAGCGCCAGGATGAGTTCAACGCCGAGGATCAGGATTGGGGCTTCGTG
GCCATGGTGATGGATCGCCTGTTCCTGTGGCTGTTCATGATCGCCAGCCTGGTGGGCACC
TTCGTGATCCTGGGCGAGGCCCCCAGCCTGTACGATGATACCAAGGCCATCGATGTGCAG
CTGAGCGATGTGGCCAAGCAGATCTACAACCTGACCGAGAAGAAGAAC
Data files
The codon usage table is read by default from "Ehum.cut" in the
'data/CODONS' directory of the EMBOSS distribution. If the name of a
codon usage file is specified on the command line, then this file will
first be searched for in the current directory and then in the
'data/CODONS' directory of the EMBOSS distribution.
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:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
"Corrupt codon index file" - the codon usage file is incomplete or
empty.
"The file 'drosoph.cut' does not exist" - the codon usage file cannot
be opened.
Exit status
This program always exits with a status of 0, unless the codon usage
table cannot be opened.
Known bugs
None.
See also
Program name Description
backtranambig Back translate a protein sequence to ambiguous codons
charge Protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
coderet Extract CDS, mRNA and translations from feature tables
compseq Count composition of dimer/trimer/etc words in a sequence
emowse Protein identification by mass spectrometry
freak Residue/base frequency table or plot
iep Calculates the isoelectric point of a protein
mwcontam Shows molwts that match across a set of files
mwfilter Filter noisy molwts from mass spec output
octanol Displays protein hydropathy
pepinfo Plots simple amino acid properties in parallel
pepstats Protein statistics
pepwindow Displays protein hydropathy
pepwindowall Displays protein hydropathy of a set of sequences
plotorf Plot potential open reading frames
prettyseq Output sequence with translated ranges
remap Display sequence with restriction sites, translation etc
showorf Pretty output of DNA translations
showseq Display a sequence with features, translation etc
sixpack Display a DNA sequence with 6-frame translation and ORFs
transeq Translate nucleic acid sequences
Author(s)
Alan Bleasby (ajb ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
History
Completed 6 Oct 1999
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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