makeprotseq 



Function

   Creates random protein sequences

Description

   Makes a set of random sequences. The sequence composition can be
   defined by reading an optional pepstats output file of protein
   composition.

Algorithm

Usage

   Here is a sample session with makeprotseq


% makeprotseq 
Creates 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 
Creates 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 standard output
   -filter             boolean    Read standard input, write 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

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 = 38590.05             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 outputs a graph to the specified graphics device. outputs
   a report format file. The default format is ...

  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
   biosed       Replace or delete sequence sections
   codcopy      Reads and writes a codon usage table
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractalign Extract regions from a sequence alignment
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Write a list file of the logical OR of two sets of sequences
   makenucseq   Creates random nucleotide sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Exclude a set of sequences and write out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   skipseq      Reads and writes (returns) sequences, skipping first few
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the 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