EMBOSS: backtranseq

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 sequence: tsw:opsd_human 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 Edrosophila.cut Back translate a protein sequence Input sequence: tsw:ach2_drome 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   Sequence USA
  [-outfile]           seqout     Output sequence USA

   Additional (Optional) qualifiers:
   -cfile              codon      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

   "-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 deaths

Standard (Mandatory) qualifiers Allowed values Default

[-sequence]
(Parameter 1) Sequence USA Readable sequence Required

[-outfile]
(Parameter 2) Output sequence USA Writeable sequence <sequence>.format

Additional (Optional) qualifiers Allowed values Default

-cfile Codon usage table name Codon usage file in EMBOSS data path Ehum.cut

Advanced (Unprompted) qualifiers Allowed values Default

(none)

Standard (Mandatory) qualifiers	Allowed values	Default
[-sequence] (Parameter 1)	Sequence USA	Readable sequence	Required
[-outfile] (Parameter 2)	Output sequence USA	Writeable sequence	<sequence>.format
Additional (Optional) qualifiers	Allowed values	Default
-cfile	Codon usage table name	Codon usage file in EMBOSS data path	Ehum.cut
Advanced (Unprompted) qualifiers	Allowed values	Default
(none)

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     STANDARD;      PRT;   348 AA.
AC   P08100; Q16414;
DT   01-AUG-1988 (Rel. 08, Created)
DT   01-AUG-1988 (Rel. 08, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   RHODOPSIN.
GN   RHO.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 84272729.
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   SEQUENCE OF 1-120 FROM N.A.
RA   BENNETT J., BELLER B., SUN D., KARIKO K.;
RL   Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   REVIEW ON ADRP VARIANTS.
RX   MEDLINE; 94004905.
RA   AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA   BHATTACHARYA S.;
RT   "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL   Hum. Mutat. 2:249-255(1993).
RN   [4]
RP   VARIANT ADRP HIS-23.
RX   MEDLINE; 90136922.
RA   DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA   YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT   "A point mutation of the rhodopsin gene in one form of retinitis
RT   pigmentosa.";
RL   Nature 343:364-366(1990).
RN   [5]
RP   VARIANTS ADRP.
RX   MEDLINE; 91051574.
RA   FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA   HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA   WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA   BHATTACHARYA S.S., HUMPHRIES P.;
RT   "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT   proline-->histidine substitution (codon 23) in pedigrees from
RT   Europe.";
RL   Am. J. Hum. Genet. 47:941-945(1990).
RN   [6]
RP   VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX   MEDLINE; 91015273.


  [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 ADRP).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (IN ADRP).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (IN ADRP).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (IN ADRP).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (IN ADRP).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       MISSING (IN ADRP).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       MISSING (IN ADRP).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (IN ADRP).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (IN ADRP).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (IN CSNB4).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (IN ADRP).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (IN ADRP).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (IN ADRP).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (IN ADRP).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (IN ADRP).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (IN ADRP).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (IN ADRP; COMMON VARIANT).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (IN ADRP).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (IN ADRP).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (IN ADRP).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
     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     STANDARD;      PRT;   576 AA.
AC   P17644;
DT   01-AUG-1990 (REL. 15, CREATED)
DT   01-AUG-1990 (REL. 15, LAST SEQUENCE UPDATE)
DT   01-NOV-1997 (REL. 35, LAST ANNOTATION UPDATE)
DE   ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR.
GN   ACRE OR SAD OR ACR96AB.
OS   DROSOPHILA MELANOGASTER (FRUIT FLY).
OC   EUKARYOTA; METAZOA; ARTHROPODA; TRACHEATA; HEXAPODA; INSECTA;
OC   PTERYGOTA; DIPTERA; BRACHYCERA; MUSCOMORPHA; EPHYDROIDEA;
OC   DROSOPHILIDAE; DROSOPHILA.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90301489.
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   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90353591.
RA   JONAS P., BAUMANN A., MERZ B., GUNDELFINGER E.D.;
RT   "Structure and developmental expression of the D alpha 2 gene
RT   encoding a novel nicotinic acetylcholine receptor protein of
RT   Drosophila melanogaster.";
RL   FEBS LETT. 269:264-268(1990).
RN   [3]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 90360975.
RA   SAWRUK E., SCHLOSS P., BETZ H., SCHMITT B.;
RT   "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD,
RT   a novel developmentally regulated alpha-subunit.";
RL   EMBO J. 9:2671-2677(1990).
CC   -!- FUNCTION: AFTER BINDING ACETYLCHOLINE, THE ACHR RESPONDS BY AN
CC       EXTENSIVE CHANGE IN CONFORMATION THAT AFFECTS ALL SUBUNITS AND
CC       LEADS TO OPENING OF AN ION-CONDUCTING CHANNEL ACROSS THE PLASMA
CC       MEMBRANE.
CC   -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC   -!- TISSUE SPECIFICITY: CNS IN EMBRYOS.
CC   -!- DEVELOPMENTAL STAGE: LATE EMBRYONIC AND LATE PUPAL STAGES.
CC   -!- SIMILARITY: BELONGS TO THE LIGAND-GATED IONIC CHANNELS FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; X52274; G7803; -.
DR   EMBL; X53583; G8533; -.
DR   PIR; S11679; ACFFA2.
DR   FLYBASE; FBgn0000039; nAcR-alpha-96Ab.
DR   PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
DR   PFAM; PF00065; neur_chan; 1.
KW   RECEPTOR; POSTSYNAPTIC MEMBRANE; IONIC CHANNEL; GLYCOPROTEIN; SIGNAL;
KW   TRANSMEMBRANE; MULTIGENE FAMILY.
FT   SIGNAL        1     41       PROBABLE.
FT   CHAIN        42    576       ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2.
FT   DOMAIN       42    261       EXTRACELLULAR (POTENTIAL).
FT   TRANSMEM    262    285       POTENTIAL.
FT   TRANSMEM    293    311       POTENTIAL.
FT   TRANSMEM    327    346       POTENTIAL.
FT   DOMAIN      347    526       CYTOPLASMIC (POTENTIAL).
FT   TRANSMEM    527    545       POTENTIAL.
FT   DISULFID    169    183       BY SIMILARITY.
FT   DISULFID    243    244       ASSOCIATED WITH RECEPTOR ACTIVATION
FT                                (BY SIMILARITY).
FT   CARBOHYD     65     65       POTENTIAL.
FT   CARBOHYD    254    254       POTENTIAL.
FT   CARBOHYD    570    570       POTENTIAL.
SQ   SEQUENCE   576 AA;  65506 MW;  7B795689 CRC32;
     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.
ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG
AGAAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG
GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC
GTGACCGTGCAGCACAAGAAGCTGAGAACCCCCCTGAACTACATCCTGCTGAACCTGGCC
GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC
GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC
GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGATACGTGGTGGTGTGC
AAGCCCATGAGCAACTTCAGATTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC
TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGATACATCCCC
GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC
GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC
TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC
GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGAATGGTGATCATCATGGTGATCGCC
TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC
AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC
TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGAAACTGCATGCTGACCACC
ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC
GAGACCAGCCAGGTGGCCCCCGCC

Output files for usage example 2

File: ach2_drome.fasta

>ACH2_DROME P17644 ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR.
ATGGCCCCCGGCTGCTGCACCACCCGCCCCCGCCCCATCGCCCTGCTGGCCCACATCTGG
CGCCACTGCAAGCCCCTGTGCCTGCTGCTGGTGCTGCTGCTGCTGTGCGAGACCGTGCAG
GCCAACCCCGACGCCAAGCGCCTGTACGACGACCTGCTGTCCAACTACAACCGCCTGATC
CGCCCCGTGTCCAACAACACCGACACCGTGCTGGTGAAGCTGGGCCTGCGCCTGTCCCAG
CTGATCGACCTGAACCTGAAGGACCAGATCCTGACCACCAACGTGTGGCTGGAGCACGAG
TGGCAGGACCACAAGTTCAAGTGGGACCCCTCCGAGTACGGCGGCGTGACCGAGCTGTAC
GTGCCCTCCGAGCACATCTGGCTGCCCGACATCGTGCTGTACAACAACGCCGACGGCGAG
TACGTGGTGACCACCATGACCAAGGCCATCCTGCACTACACCGGCAAGGTGGTGTGGACC
CCCCCCGCCATCTTCAAGTCCTCCTGCGAGATCGACGTGCGCTACTTCCCCTTCGACCAG
CAGACCTGCTTCATGAAGTTCGGCTCCTGGACCTACGACGGCGACCAGATCGACCTGAAG
CACATCTCCCAGAAGAACGACAAGGACAACAAGGTGGAGATCGGCATCGACCTGCGCGAG
TACTACCCCTCCGTGGAGTGGGACATCCTGGGCGTGCCCGCCGAGCGCCACGAGAAGTAC
TACCCCTGCTGCGCCGAGCCCTACCCCGACATCTTCTTCAACATCACCCTGCGCCGCAAG
ACCCTGTTCTACACCGTGAACCTGATCATCCCCTGCGTGGGCATCTCCTACCTGTCCGTG
CTGGTGTTCTACCTGCCCGCCGACTCCGGCGAGAAGATCGCCCTGTGCATCTCCATCCTG
CTGTCCCAGACCATGTTCTTCCTGCTGATCTCCGAGATCATCCCCTCCACCTCCCTGGCC
CTGCCCCTGCTGGGCAAGTACCTGCTGTTCACCATGCTGCTGGTGGGCCTGTCCGTGGTG
ATCACCATCATCATCCTGAACATCCACTACCGCAAGCCCTCCACCCACAAGATGCGCCCC
TGGATCCGCTCCTTCTTCATCAAGCGCCTGCCCAAGCTGCTGCTGATGCGCGTGCCCAAG
GACCTGCTGCGCGACCTGGCCGCCAACAAGATCAACTACGGCCTGAAGTTCTCCAAGACC
AAGTTCGGCCAGGCCCTGATGGACGAGATGCAGATGAACTCCGGCGGCTCCTCCCCCGAC
TCCCTGCGCCGCATGCAGGGCCGCGTGGGCGCCGGCGGCTGCAACGGCATGCACGTGACC
ACCGCCACCAACCGCTTCTCCGGCCTGGTGGGCGCCCTGGGCGGCGGCCTGTCCACCCTG
TCCGGCTACAACGGCCTGCCCTCCGTGCTGTCCGGCCTGGACGACTCCCTGTCCGACGTG
GCCGCCCGCAAGAAGTACCCCTTCGAGCTGGAGAAGGCCATCCACAACGTGATGTTCATC
CAGCACCACATGCAGCGCCAGGACGAGTTCAACGCCGAGGACCAGGACTGGGGCTTCGTG
GCCATGGTGATGGACCGCCTGTTCCTGTGGCTGTTCATGATCGCCTCCCTGGTGGGCACC
TTCGTGATCCTGGGCGAGGCCCCCTCCCTGTACGACGACACCAAGGCCATCGACGTGCAG
CTGTCCGACGTGGCCAAGCAGATCTACAACCTGACCGAGAAGAAGAAC

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.

To see the available EMBOSS codon usage files, run:


% embossdata -showall

To fetch one of the codon usage tables (for example 'Emus.cut') into your current directory for you to inspect or modify, run:


% embossdata -fetch -file Emus.cut

Most, but not all of tehse files are derived from those supplied on the EBI ftp server and are described in the README file from ftp://ftp.ebi.ac.uk/pub/databases/codonusage

If you are confused by the file names, you are best getting the CUTG database from that server (ftp://ftp.ebi.ac.uk/pub/databases/cutg/) and then running the emboss program 'cutgextract'. The filenames produced will be descriptive (and therefore long). You'd best do that in a new directory as a lot of files are produced.

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.

Program name	Description
charge	Protein charge plot
checktrans	Reports STOP codons and ORF statistics of a protein
coderet	Extract CDS, mRNA and translations from feature tables
compseq	Counts the 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 a sequence with restriction cut 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 (ableasby © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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.

Function

Description

Codon usage table name

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tsw:opsd_human

Input files for usage example 2

Database entry: tsw:ach2_drome

Output file format

Output files for usage example

File: opsd_human.fasta

Output files for usage example 2

File: ach2_drome.fasta

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments