|   | makeprotseq | 
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
| % 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
| 
   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  [ | 
| 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) | |||
| PEPSTATS of LACI_ECOLI from 1 to 360 Molecular weight = 38590.06 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 | 
| >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 | 
| >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 | 
| 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 | 
| pasteseq | Insert one sequence into another | 
| revseq | Reverse and complement a nucleotide sequence | 
| seqret | Reads and writes (returns) 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 | 
| 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 |