| 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

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
      [-outfile]           seqout     Output sequence USA

       Optional qualifiers:
       -cfile              codon      Codon usage table name

       Advanced qualifiers: (none)
       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
[-outfile] (Parameter 2) | Output sequence USA | Writeable sequence | <sequence>.format
Optional qualifiers | Allowed values | Default
-cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehum.cut
Advanced 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

Not every file but most are described in the README file from ftp://ftp.ebi.ac.uk/pub/databases/codonusage

You can use the EMBOSS program 'cutgextract' on the CUTG database to get files with more meaningful (long) names.

## 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
--- | ---
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 © hgmp.mrc.ac.uk)
HGMP-RC, 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.

## Comments