                                 makeprotseq



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Create random protein sequences

Description

   makeprotseq writes an output file with a set of random protein
   sequences. The sequence composition is defined from reading a pepstats
   output file of protein composition: the sequences are created with
   amino acid frequencies matching those given in the file. The number of
   sequences to create and length of each sequence is specified.
   Optionally, a user-defined string may be inserted into each output
   sequence at a specified position

Algorithm

Usage

   Here is a sample session with makeprotseq


% makeprotseq
Create random protein sequences
Pepstats program output file (optional):
Number of sequences created [100]:
Length of each sequence [100]:
protein output sequence(s) [makeseq.fasta]:


   Go to the output files for this example

   Example 2


% makeprotseq
Create random protein sequences
Pepstats program output file (optional): ../pepstats-keep/laci_ecoli.pepstats
Number of sequences created [100]:
Length of each sequence [100]:
protein output sequence(s) [makeseq.fasta]:


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

Command line arguments

Create random protein sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
   -pepstatsfile       infile     This file should be a pepstats output file.
                                  Protein sequences will be created with the
                                  composition in the pepstats output file.
   -amount             integer    [100] Number of sequences created (Integer 1
                                  or more)
   -length             integer    [100] Length of each sequence (Integer 1 or
                                  more)
*  -insert             string     String that is inserted into sequence (Any
                                  string)
*  -start              integer    [1] Start point of inserted sequence
                                  (Integer 1 or more)
  [-outseq]            seqoutall  [.] Protein sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -useinsert          toggle     [N] Do you want to make an insert

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outseq" associated qualifiers
   -osformat1          string     Output seq format
   -osextension1       string     File name extension
   -osname1            string     Base file name
   -osdirectory1       string     Output directory
   -osdbname1          string     Database name to add
   -ossingle1          boolean    Separate file for each entry
   -oufo1              string     UFO features
   -offormat1          string     Features format
   -ofname1            string     Features file name
   -ofdirectory1       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


Input file format

   makeprotseq reads a pepstats output file.

  Input files for usage example 2

  File: ../pepstats-keep/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 = 6.8385
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


Output file format

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Output files for usage example

  File: makeseq.fasta

>EMBOSS_001
nrvlhpepnprtdniytpawirllygvwvwnrqachnkeerkryppklmmydsqfwcdfe
wadccspkqgwhgnlvkvnrteemfgmqflpqvhpgkkvd
>EMBOSS_002
vtvkddwhkdwwcrpamdylhywlkqrnhytdlslyyttstprwarmadtflapegndcv
qtmywrwvndgdivclecqvcgrfdiymvqdsgqidkghs
>EMBOSS_003
celpniypyweragingdwhetvtvrmhcnnddilwyqmnykppsshavhyivwrrnwcw
nfidqgdgdnrncmnytsnapeqksqlkyghkrqftvvvr
>EMBOSS_004
cshpdepancgridtykhvaydmtdtkaeyhgsspelqslrqkfsnqvwhnraviwwehp
iqdcrlkhselrchskhlseikmpvevtmsdwlmytgyfm
>EMBOSS_005
cpcqytiqygsdlfldsqmpkckkisvelvclvynaqsnlsyfiheaafmvfhpfsllci
meecinwincriaiwppkfvqleidkmiwkvklqcknvcw
>EMBOSS_006
ifawkitieywnktydldkmrklakdfgfppfdpwpihvgccnisnwfmepkfwaqmkcw
mstltiedndwlmlnttefgeqllfywmhwmpcqdewqph
>EMBOSS_007
eiviqqfmvshealkqlgnkwnsqqmhvndriydvkhlvdasnfihhplnkryfrenvns
tacccvhtwsipclfqtidhivnldgaygpwyrvkyshsp
>EMBOSS_008
hmcmmmshfyvgycffvsvrdqrqtceyphvlmhnilftqgralwvrskqpqcadnhqpk
ghwwvawrlqsymkgpqykpqkdwwqgkkffghiwemvrc
>EMBOSS_009
rwydtkfimsgkfaysarqyprqikegeatalrsgpqicpaewiaanypgasfekrqfmd
mqwicgyeprehrwsekymshesvkkgyrhglkngveyqt
>EMBOSS_010
yatmyyygtgmtmkwgepiyvaqflirneqepkvkhahghdascrpkirldlfleerpnp
yksvsfnrfyaggkliigiitydttchkihahdrkeekar
>EMBOSS_011
arakqhrkhmlvknsanwayqswdgkskllvtfghvmenmfkhwrkrsmncvrpinrhfe
gpvmigvkadcqghgqidniqcawpnfedmhamrtvqqvm
>EMBOSS_012
dkihtlrhnhypshmtmtewetvvgvfmipcsmariscpvwgnwphmqglcyppwsgtpn
esqgctnnitfwmnwvspywlfpdlpnfatfmtlgnqrfh
>EMBOSS_013
fkghwqakfphwlsydlkitkyftrqfhmnfiarmngasnfhgrsriawmahlwnqhara
qaflmrlstheyewyfrnqapldqlfnecvlpvmsawhmw
>EMBOSS_014
shhsqgkrnnectscqdqagfdcadnfttqvmekhwtheifnhivgisaittthyvytmt
wcqsfsnmnnlwsragchwevdiagvrmmdicfsvyercf
>EMBOSS_015
hknwdqldarqikalervvclpcenqvidtmvvglifkkkdlfmintwqtwkgisvysci
hqfligfinkgwfpdaysvgvlmfdqdaienadahgdhhl
>EMBOSS_016
gwylwhlgntdaqfeghstgnvhhedkathldfyhedwgchnrtqppvfgmanrwdvakk
seygwmvgfhqcddtlgyfemfhawywgypgcdfhfnrpp
>EMBOSS_017
lfqtfqvwnaymgcgryaclewysaisgcsvmqfgdfkdpifhfptdrlwggiesgdkev


  [Part of this file has been deleted for brevity]

>EMBOSS_084
yscilavytfadkdtptkkapetdlnpdhermykmhdhsrtghwtrnnigcksssyisqv
tciplripvnfrlvvawrcwmdlqddwkphmnmffmrray
>EMBOSS_085
iivhagtkvksgdpaiglirectikwcemwpdsicdtfkivkyfiqskttmqsyyvnilr
lsravaskdsqetdtcgdsmdmshvcpkchqnwhslgsdh
>EMBOSS_086
frqhcqqnsdvfqyrhwktfpfryakchgihvwpkptmeccwlprhqwkktnrvnpvlnf
ytdhhkviceqlelvvsykhskdrvthqmprrnvgegqdw
>EMBOSS_087
ctedmshteihecsmfddlrdwhmkrdcsipnagrkkegwipkldmmrycvylqipktti
fhdvsatcvasfmvhkpndfmlckrciyhykgdtwwrpwt
>EMBOSS_088
ygscslkqtqlgsggkehqqqyleqayewavmisgspnciqsepwmmsmgkpkfwivryn
yekcvmdgyacfqkwegpdhwvsvvhrkmydrggffylge
>EMBOSS_089
hhqkiqscaitwtgiinqqwfmmnrrgwakkqdhqasafvitdnkrswtreyfnkmvism
mkmhcvqtnvhcsaqrrsmhtppyntlitvprmgcpyfka
>EMBOSS_090
akrdfsklilitwvlhficlrfgafaffgmemailrpsdqiywsnmqhnamfkptdhmlv
pelycargfavhpadqgghwwlderteiphyrikdrshde
>EMBOSS_091
pyrehgtmcpckvwqcplydgtadsrgagywpsfhneppqgvseiefeccmaciqqctka
ffqgdamkkkylqnqevptpypdhildnmlqsvyqggqsq
>EMBOSS_092
alhntshnerdmetlwgagcfivemkahfvcyelrkgcrcrrsfnvkfhahaqdwwffmd
snptmgncgeqltgpkqhadilfidinqmmctmchchqye
>EMBOSS_093
aflkktaalkrfrmmtvtmvnqlwcagatifmhilkdlsrsmilgrhcegmwillcfasy
ralvkvdsgtkrwwhkdflelywwdeayrhysetqyasav
>EMBOSS_094
rshvqnvdhpssidmkripdwtcqglqmqinlwllrragirravmykiwdkgemnvelah
iwayhgfrsfikfgqpiqkmrvmyerilptdllyiedcnh
>EMBOSS_095
yenmtynnavemahpeirnwlwrsgfdpmgvhchladnppvscatlvmklwitnfwaaqy
pvwnqfltcyqmprqleflrglvgnchhdrwwqdalitrt
>EMBOSS_096
rdhgrspnwmkftvgvdmtalmycwrdrlewliacfhftmkrgkciewmselicppptnf
vqisnrcmsirgwmymradkeaqcnirwyiyahlkhkwgm
>EMBOSS_097
aygfwfqqhhhfeptkqpeylawqtwtcvkkrcqsytachfeqvthvnkcpsqpiapced
dpsptitsssscnierktgigltcysnhgalmritpkyci
>EMBOSS_098
vaaiydmiaqwvviqtwfvttddqerclwwesrhqyydeyeffftistpvwcyprrrlia
ghaqvikywawvdeslipsefqqapeipdpigpgkvqpeq
>EMBOSS_099
vlmpqdsprpefivnvfntadpscecsckfqlfmcekffncikangvnvdmpchipkaam
tecytlqiawppqnkltypgvhtksfgeewldhmpieqgg
>EMBOSS_100
seffvlpnicymnwnramyvfshwwycfpcsymkdklfwdtrypqihpapklnmedacpg
ytctrpqryqilarqtwyarkhygwvnwtdiascntmdgq

  Output files for usage example 2

  File: makeseq.fasta

>EMBOSS_001
eqngievefrcplriaaeyahqsgatanpaedqllifgvlqsqaerggfgavpdkallvv
nllvlargqkaikegpsaecpvlgttgqtgrdntekssnv
>EMBOSS_002
npnsvlatsvmavqeyslmgtmagsqdriaavgagmapaaprcmydsllavglrvkevln
qaranqnaelilialsvlqnltqvvsarpqlqtqilhtta
>EMBOSS_003
llgersmqmmvdyksrivatvaapndgtveevligamdgemhrraqiyataipnqqrmln
rlhldiltlrdevgrmpaeyevqgadghlkihcdkpappq
>EMBOSS_004
laielvelevkdhvaasinlmlgavagylmttqaevgqqsqqglprdaairqyasmavtr
sdlvcgsiqvgqvtasisplsssravapgqvassmatakr
>EMBOSS_005
vevqaphdmtavsksvqdfrsvhssqavgalsalryqaegqmksivyllfaktrvpssli
flvlsrmseldsysaeqsvaqglhvsginsagsdwhrnla
>EMBOSS_006
ivynsspslmnfgamlglsgdhsygvktleelvrnrhtailvrsqeavsvrhvnldfgva
fqagpsvlelngrgeaalvtlqsgkmmginsevqllndei
>EMBOSS_007
vsaiqdkgaqillssqstrgaraqqftarvqhlvagtsnlyqrvhttegegdaldvepea
allvvaipnqievgvqahvthargltlatealqpglatqr
>EMBOSS_008
iglrssattmniawklaaaqlqqdpllmqingfifiglaqidysnnqasqrdvlleidqh
kimmnyadsqalshkrqmsedglanqtghvkttsnvgnql
>EMBOSS_009
qallaskifqtsklaqyqdaqqdssltvlpygcqieqslrlvaiyyrldtlpvvgddvsv
rqasvtavdqliqaalgaraivqasgtmditggriplaqa
>EMBOSS_010
myafmmakatgpssatvqianydkgsceldlegasiytkilypvqrsidslgvsvvqqre
asaaavrqkmlktssihkisamvpavtssilivdgllslq
>EMBOSS_011
lclgdiqsiggngfqyraymdaalksagggppvtiafleglstndsdagfvpqrifqikv
idpssiaslllqtitdslridlyarrvvlrtygdpnddas
>EMBOSS_012
lssiagdiriarqtspgavmlanpkpvgirlasyqsaleaatraeirdtglarraatpqe
vqdtvaeesavasranpemasvqvgeeklavfpgirdqkt
>EMBOSS_013
ksitaqyhvetngpmlghsasmvpqdktgrviydrrtyarkitdqdslagytgmrqiyql
qwvggdsqatvalaatcrdlqgldskrvvagdpgqyaisn
>EMBOSS_014
atiadkgdrrvlppvqldlkkllylrkaadagvstnptvsleiiaksqlspaptanapsp
aldqkqrgffgaaqyivtnlplswkaqgsvsvvqpmvdvl
>EMBOSS_015
igeavdgllddhslgldaplselvrqnhlasnntgskhshlsksheaadaagthaaacls
tqksstkseskakrlyaqatagflvqlysvrlvlttltts
>EMBOSS_016
inagntgtealydkvtiaatrattvvsypiglkaivlmivirqpqrqavtryednlawsg
avmiasaikidlvvpsiaklrvtlmmakaekvlkitrdre
>EMBOSS_017
gvqpvqaarlasiliqalvsvnmqysqtvqarqktlkhvesltlqplqgaktslptvgln


  [Part of this file has been deleted for brevity]

>EMBOSS_084
mqvsgynaavlvslpepsgyevpvsreltvdsasrivtaqaitaadresivgppqmipda
alsrgqhenrlqsaalmdwnsvsqvlasrifrgvkfddla
>EMBOSS_085
hsailtasngatvelhtsiqlvpssallgaevqslvpvhhasakhqchppsqammarssd
gqqyayphvadlplalklqrlsaiavqgliqfaiasiqli
>EMBOSS_086
kqdtwdqrqlakqmqtasakrkqmygvtthinmehrpslvvasectqashprdpernsrv
maliisnslvdglsaaqmhiasldaatdsecqeptvkqva
>EMBOSS_087
valvgqtavitvlprkvvgdvatssqllqsqeltcssvtniegglrrqmvnagqhqsapi
livnalplalavsptserllsgvsdvsmiastvpnnqeaa
>EMBOSS_088
atalqgsqaqskattsvtqddagvdlavalashpkaerlsdaleargagthrslnsaqae
mlgvpfviallldgmvievtanapntdhgmlditvvastv
>EMBOSS_089
ttqsidalyhpmaiiirdqnvgfeqdknlgsdviqlqyvnsplegcqnpqlmkrgrasqr
ssriwpdaraivqydqqagtpedmrpssparqftlellgy
>EMBOSS_090
yhdltqsgissanngtkiwgqvklvylktglfyssdeqvqsmnqrgdielrvgepvtssn
qvsmlldiklptrlvqktimasvvdalhriaqhhvqqilv
>EMBOSS_091
eacvtkaglrvgpnqlegmltpwvadklkaarqvielerdiaavhlvlvlryvsqqvahy
vkqtllggsgmgdrdvneprmdvisgvegsdqnlqtkqqd
>EMBOSS_092
lgieaqtrvdvglpsniltlvsnvgsytkalmvgqgilqlqqpkraskiliyqvmntvgl
cedagielilqsatqsqtylhsvilsrqrflpgvtliqav
>EMBOSS_093
lvghhalyshdvqsgpnpsafqsnlytypivgihssvspqqssskdtlvtsmssswvyaa
dygpgalptpsqantsltglsaamvlymdiaalaqayala
>EMBOSS_094
qqindeavteaqhvrhqselapvqksdrqsrsnssqqlticdyarmsinvhivreavslt
inymitvqakisvkdqsqssdagmvqigrpvggmsvvvft
>EMBOSS_095
mlrgpaerypvgyievscrngaqqikvrrinilisyvreeaqvyagarsgasaelayydl
eanrqkspvadrqqqslvgqkgairvtildnaqvlsspqp
>EMBOSS_096
qvtiqqeensgvpakavgplggavaqlcslmgillvtkasgdtslivmsplghledrprv
nqsardwgqsqkasarqlvgvldlricamhmytsgignts
>EMBOSS_097
lmtkavqqtitkvqagdrlasyndamalaghqvdqaayvtkvdppinrhleaqqsyelvv
leqrpspqaqalrsvdsptstgpvmariilggqspesals
>EMBOSS_098
nlyhmvrswqaaasqpmvapalvqvcvganvqdtdmmvvmvtkkpsqpenavaddqqssl
tiyqasslmlnnllagiqavlddlqvsdvrhtrtsndrld
>EMBOSS_099
ngredlqedrvvsnrakrawveplvvqwhvdsvgllgvlelhglrkneavgrvihegyls
pllaagdslnqrqrgsamekatpsqtklvnglifeildtt
>EMBOSS_100
plklpgqfslafrnedlgmnkqtanmlkevqmsslggkavpdaeditelegseflvwldt
mpvaqqddadhgldqanaydhiminpraplilqleasltq

Data files

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makenucseq       Create random nucleotide sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   This application was contributed by Henrikki Almusa, Medicel, Helsinki,
   Finland

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

History

Target users

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

Comments

   None
