makeprotseq
Wiki
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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:6.5.6.0
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 = 6.8820
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
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