makeprotseq

 

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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

   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 is accepted)
*  -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. 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

Standard (Mandatory) qualifiers Allowed values Default
-pepstatsfile This file should be a pepstats output file. Protein sequences will be created with the composition in the pepstats output file. Input file Required
-amount Number of sequences created Integer 1 or more 100
-length Length of each sequence Integer 1 or more 100
-insert String that is inserted into sequence Any string is accepted An empty string is accepted
-start Start point of inserted sequence Integer 1 or more 1
[-outseq]
(Parameter 1)
Protein sequence set(s) filename and optional format (output USA) Writeable sequence(s) <*>.format
Additional (Optional) qualifiers Allowed values Default
-useinsert Do you want to make an insert Toggle value Yes/No No
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

makeprotseq reads any normal sequence USAs.

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 = 6.8820
A280 Molar Extinction Coefficient  = 21620   
A280 Extinction Coefficient 1mg/ml = 0.56      
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

makeprotseq writes a sequence file with the number of sequences requested.

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 Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Removes a section from a sequence
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieves 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 Reads and writes a feature table
featreport Reads and writes a feature table
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
maskambignuc Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks 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 all 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 Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of sequences
seqretsplit Reads sequences and writes them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) 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 Removes 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

History

Target users

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

Comments

None