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:6.4.0.0 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 = 6.8820 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 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 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 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 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 seqcount Reads and counts sequences 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 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