EMBOSS: pepstats

| pepstats

## Wiki

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## Function

Calculate statistics of protein properties

## Description

pepstats reads one or more protein sequences and writes an output file with various statistics on the protein properties. This includes:

- Molecular weight
- Number of residues
- Average residue weight
- Charge
- Isoelectric point
- For each type of amino acid: number, molar percent, DayhoffStat
- For each physico-chemical class of amino acid: number, molar percent
- Probability of protein expression in E. coli inclusion bodies
- Molar extinction coefficient (A280)
- Extinction coefficient at 1 mg/ml (A280)

## Usage

Here is a sample session with pepstats

    % pepstats
    Calculate statistics of protein properties
    Input protein sequence(s): tsw:laci_ecoli
    Pepstats program output file [laci_ecoli.pepstats]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Calculate statistics of protein properties
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Protein sequence(s) filename and optional
                                      format, or reference (input USA)
      [-outfile]           outfile    [*.pepstats] Pepstats program output file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -aadata             datafile   [Eamino.dat] Amino acid properties
       -mwdata             datafile   [Emolwt.dat] Molecular weight data for amino
                                      acids
       -[no]termini        boolean    [Y] Include charge at N and C terminus
       -mono               boolean    [N] Use monoisotopic weights

       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
       -scircular1         boolean    Sequence is circular
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -odirectory2        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

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
[-outfile] (Parameter 2) | outfile | Pepstats program output file | Output file | <*>.pepstats
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-aadata | datafile | Amino acid properties | Data file | Eamino.dat
-mwdata | datafile | Molecular weight data for amino acids | Data file | Emolwt.dat
-[no]termini | boolean | Include charge at N and C terminus | Boolean value Yes/No | Yes
-mono | boolean | Use monoisotopic weights | 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
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-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 |
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | 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

## Input file format

pepstats reads one or more protein sequences.

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.

### Input files for usage example

'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:laci_ecoli

    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   13-JUN-2012, entry version 136.
    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
    //

## Output file format

### Output files for usage example

### File: laci_ecoli.pepstats

    PEPSTATS of LACI_ECOLI from 1 to 360

    Molecular weight = 38590.16  		Residues = 360
    Average Residue Weight  = 107.195 	Charge   = 1.5
    Isoelectric Point = 6.8820
    A280 Molar Extinction Coefficients  = 22920 (reduced)   23045 (cystine bridges)
    A280 Extinction Coefficients 1mg/ml = 0.594 (reduced)   0.597 (cystine bridges)
    Improbability of expression in inclusion bodies = 0.660

    Residue		Number		Mole%		DayhoffStat
    A = Ala		44		12.222 		1.421
    B = Asx		0		0.000  		0.000
    C = Cys		3		0.833  		0.287
    D = Asp		17		4.722  		0.859
    E = Glu		15		4.167  		0.694
    F = Phe		4		1.111  		0.309
    G = Gly		22		6.111  		0.728
    H = His		7		1.944  		0.972
    I = Ile		18		5.000  		1.111
    J = ---		0		0.000  		0.000
    K = Lys		11		3.056  		0.463
    L = Leu		41		11.389 		1.539
    M = Met		10		2.778  		1.634
    N = Asn		12		3.333  		0.775
    O = ---		0		0.000  		0.000
    P = Pro		14		3.889  		0.748
    Q = Gln		28		7.778  		1.994
    R = Arg		19		5.278  		1.077
    S = Ser		32		8.889  		1.270
    T = Thr		19		5.278  		0.865
    U = ---		0		0.000  		0.000
    V = Val		34		9.444  		1.431
    W = Trp		2		0.556  		0.427
    X = Xaa		0		0.000  		0.000
    Y = Tyr		8		2.222  		0.654
    Z = Glx		0		0.000  		0.000

    Property	Residues		Number		Mole%
    Tiny		(A+C+G+S+T)		120		33.333
    Small		(A+B+C+D+G+N+P+S+T+V)	197		54.722
    Aliphatic	(A+I+L+V)		137		38.056
    Aromatic	(F+H+W+Y)		21		 5.833
    Non-polar	(A+C+F+G+I+L+M+P+V+W+Y)	200		55.556
    Polar		(D+E+H+K+N+Q+R+S+T+Z)	160		44.444
    Charged		(B+D+E+H+K+R+Z)		69		19.167
    Basic		(H+K+R)			37		10.278
    Acidic		(B+D+E+Z)		32		 8.889

## Data files

The Dayhoff statistic is read from the EMBOSS data file 'Edayhoff.freq'. You can inspect and modify this file by copying it into your current directory with the command: 'embossdata -fetch'.

Absorption coefficients use values read from the EMBOSS data file 'Eamino.dat'. Values in this file assume cysteines are reduced. If cysteines are in disulphide bridges the value should be adjusted as documented at the top of the file, and a local copy used to override the default values.

Molecular weights are read from a local data file Emolwt.dat.

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

DayhoffStat is the amino acid's molar percentage divided by the Dayhoff statistic. The Dayhoff statistic is read from the EMBOSS data file `Edayhoff.freq` and is the amino acid's relative occurence per 1000 aa normalised to 100.

The probability of expression in inclusion bodies is sometimes referred to as a type of solubility measure. If, however, a recombinant protein is expressed in Escherichia coli, it can be expressed as soluble in the cytosol or insoluble in inclusion bodies. If the Harrison model predicts a given protein to be probably expressed in includion bodies, this doesn't mean that it is not possible to get it soluble in the cytosol. One example: Thermatoga maritima cell divison protein FtsA with a C-terminal His-Tag has a 58% Harrison probability of being expressed in inclusion bodies. However, there was plenty of soluble protein in the E. coli cytosol (F. van den Ent and J. Lowe, EMBO J. 19, 5300-5307 2000). If the protein is expressed in inclusion bodies or not is not only dependent on the sequence, but also on many other factors, such as E. coli strain, incubation temperature, type of expression vector, strength of promoter and medium.

## References

1. Roger G. Harrison "Expression of soluble heterologous proteins via fusion with NusA protein" in inNovations 11, June 2000, p 4 - 7.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq | Back-translate a protein sequence to a nucleotide sequence
charge | Draw a protein charge plot
compseq | Calculate the composition of unique words in sequences
emowse | Search protein sequences by digest fragment molecular weight
freak | Generate residue/base frequency table or plot
hmoment | Calculate and plot hydrophobic moment for protein sequence(s)
iep | Calculate the isoelectric point of proteins
mwcontam | Find weights common to multiple molecular weights files
mwfilter | Filter noisy data from molecular weights file
octanol | Draw a White-Wimley protein hydropathy plot
oddcomp | Identify proteins with specified sequence word composition
pepdigest | Report on protein proteolytic enzyme or reagent cleavage sites
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepwindow | Draw a hydropathy plot for a protein sequence
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount | Count and extract unique words in molecular sequence(s)

## Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

Written (1999) - Alan Bleasby

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None