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Gentoo's Bugzilla – Attachment 102270 Details for
Bug 153766
Stabilisation request for EMBOSS 4.0.0 and related packages
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Another emboss test suite output
emboss.out (text/plain), 6.85 KB, created by
Michael Weyershäuser
on 2006-11-18 06:57:55 UTC
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Description:
Another emboss test suite output
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Creator:
Michael Weyershäuser
Created:
2006-11-18 06:57:55 UTC
Size:
6.85 KB
patch
obsolete
> [32;01m*[0m EMBOSS version (from "embossversion"): 4.0.0 > > [32;01m*[0m Use "seqret" to store a sequence in GenBank format, in lowercase. > [32;01m*[0m Add a title using "descseq" and convert to Fasta format. Print it > [32;01m*[0m on screen in EMBL format. > >ID PhiKZ-ORF144 standard; DNA; UNC; 783 BP. >DE Putative endolysin, complete CDA >SQ Sequence 783 BP; 254 A; 146 C; 151 G; 232 T; 0 other; > atgaaagtat tacgcaaagg cgataggggt gatgaggtat gtcaactcca gacactctta 60 > aatttatgtg gctatgatgt tggaaagcca gatggtattt ttggaaataa cacctttaat 120 > caggtagtta aatttcaaaa agataattgt ctagatagtg atggtattgt aggtaagaat 180 > acttgggctg aattattcag taaatattct ccacctattc cttataaaac tatccctatg 240 > ccaactgcaa ataaatcacg tgcagctgca actccagtta tgaatgcagt agaaaatgct 300 > actggcgttc gtagccagtt gctactaaca tttgcttcta ttgaatcagc attcgattac 360 > gaaataaaag ctaagacttc atcagctact ggttggttcc aattccttac tggaacatgg 420 > aaaacaatga ttgaaaatta tggcatgaag tatggcgtac ttactgatcc aactggggca 480 > ttacgtaaag atccacgtat aagtgcttta atgggtgccg aactaattaa agagaatatg 540 > aatattcttc gtcctgtcct taaacgtgaa ccaactgata ctgatcttta tttagctcac 600 > ttctttgggc ctggtgcagc ccgtcgtttc ctgaccactg gccagaatga attagctgct 660 > acccatttcc caaaagaagc tcaggcaaac ccatctattt tttataacaa agatgggtca 720 > cctaaaacca ttcaagaagt ttataactta atggatggta aagttgcagc acatagaaaa 780 > taa 783 >// > > [32;01m*[0m Search for common restriction sites (using "restrict" and the Rebase > [32;01m*[0m database). We expect to find only a few since viral DNA has evolved to > [32;01m*[0m protect itself from restriction enzymes. (There is only one hit, for > [32;01m*[0m the EcoRII enzyme, starting at 610.) > >######################################## ># Program: restrict ># Rundate: Sat Nov 18 2006 15:56:15 ># Commandline: restrict ># -auto ># -enzymes BamHI, EcoRI, EcoRII ># -sitelen 4 ># [-sequence] phikz-lys.fasta ># [-outfile] stdout ># Report_format: table ># Report_file: stdout >######################################## > >#======================================= ># ># Sequence: PhiKZ-ORF144 from: 1 to: 783 ># HitCount: 1 ># ># Minimum cuts per enzyme: 1 ># Maximum cuts per enzyme: 2000000000 ># Minimum length of recognition site: 4 ># Blunt ends allowed ># Sticky ends allowed ># DNA is linear ># Ambiguities allowed ># >#======================================= > > Start End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev > 610 614 EcoRII CCWGG 609 614 . . > >#--------------------------------------- >#--------------------------------------- > > [32;01m*[0m Could we mutate the sequence to make the viral DNA even more robust to > [32;01m*[0m restriction systems whilst keeping the same translation product? This > [32;01m*[0m is investigated using "recoder". (There are seven possible mutations.) > >######################################## ># Program: recoder ># Rundate: Sat Nov 18 2006 15:56:15 ># Commandline: recoder ># -auto ># -enzymes EcoRII ># [-sequence] phikz-lys.fasta ># [-outfile] stdout ># Report_format: table ># Report_file: stdout >######################################## > >#======================================= ># ># Sequence: PhiKZ-ORF144 from: 1 to: 783 ># HitCount: 7 ># ># KEY: ># Dir: Direction (Rev for reverse complement) ># EnzymeName: Enzyme name ># RS-Pattern: Restriction enzyme recognition site pattern ># Base-Posn: Position of base to be mutated ># AAs: Amino acid. Original sequence(.)After mutation ># Mutation: The base mutation to perform ># ># Creating silent mutations ># >#======================================= > > Start End Dir EnzymeName RS-Pattern Base-Posn AAs Mutation > 610 614 . EcoRII CCWGG 612 P.P T->G > 610 614 . EcoRII CCWGG 612 P.P T->C > 614 610 Rev EcoRII CCWGG 610 R.R G->A > 614 610 Rev EcoRII CCWGG 612 R.R A->C > 614 610 Rev EcoRII CCWGG 613 T.T C->G > 614 610 Rev EcoRII CCWGG 613 T.T C->A > 614 610 Rev EcoRII CCWGG 613 T.T C->T > >#--------------------------------------- >#--------------------------------------- > > [32;01m*[0m Translate gene to protein sequence. We trim the termination "*" > [32;01m*[0m character from the end of the translation. We use "transeq". The > [32;01m*[0m translation product is printed on screen in SwissProt format. > >ID PhiKZ-ORF144_1 STANDARD; PRT; 260 AA. >DE Putative endolysin, complete CDA >SQ SEQUENCE 260 AA; 28816 MW; BD21361996EBBEAB CRC64; > MKVLRKGDRG DEVCQLQTLL NLCGYDVGKP DGIFGNNTFN QVVKFQKDNC LDSDGIVGKN > TWAELFSKYS PPIPYKTIPM PTANKSRAAA TPVMNAVENA TGVRSQLLLT FASIESAFDY > EIKAKTSSAT GWFQFLTGTW KTMIENYGMK YGVLTDPTGA LRKDPRISAL MGAELIKENM > NILRPVLKRE PTDTDLYLAH FFGPGAARRF LTTGQNELAA THFPKEAQAN PSIFYNKDGS > PKTIQEVYNL MDGKVAAHRK >// > > [32;01m*[0m Show a few basic statistics about the protein using "pepstats". > [32;01m*[0m Molecular weight of the protein is 28814.90 Da (in 260 residues). > [32;01m*[0m Create an hydropathy plot in PNG format to search for transmembrane > [32;01m*[0m helices. The PNG graph shows three maxima at around residues 75, 100 > [32;01m*[0m and 135. > >PEPSTATS of PhiKZ-ORF144_1 from 1 to 260 > >Molecular weight = 28814.90 Residues = 260 >Average Residue Weight = 110.827 Charge = 7.5 >Isoelectric Point = 9.4289 >A280 Molar Extinction Coefficient = 28590 >A280 Extinction Coefficient 1mg/ml = 0.99 >Improbability of expression in inclusion bodies = 0.866 > >Residue Number Mole% DayhoffStat >A = Ala 23 8.846 1.029 >B = Asx 0 0.000 0.000 >C = Cys 3 1.154 0.398 >D = Asp 14 5.385 0.979 >E = Glu 12 4.615 0.769 >F = Phe 13 5.000 1.389 >G = Gly 20 7.692 0.916 >H = His 3 1.154 0.577 >I = Ile 12 4.615 1.026 >J = --- 0 0.000 0.000 >K = Lys 21 8.077 1.224 >L = Leu 22 8.462 1.143 >M = Met 8 3.077 1.810 >N = Asn 16 6.154 1.431 >O = --- 0 0.000 0.000 >P = Pro 15 5.769 1.109 >Q = Gln 9 3.462 0.888 >R = Arg 11 4.231 0.863 >S = Ser 12 4.615 0.659 >T = Thr 21 8.077 1.324 >U = --- 0 0.000 0.000 >V = Val 13 5.000 0.758 >W = Trp 3 1.154 0.888 >X = Xaa 0 0.000 0.000 >Y = Tyr 9 3.462 1.018 >Z = Glx 0 0.000 0.000 > >Property Residues Number Mole% >Tiny (A+C+G+S+T) 79 30.385 >Small (A+B+C+D+G+N+P+S+T+V) 137 52.692 >Aliphatic (I+L+V) 47 18.077 >Aromatic (F+H+W+Y) 28 10.769 >Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 141 54.231 >Polar (D+E+H+K+N+Q+R+S+T+Z) 119 45.769 >Charged (B+D+E+H+K+R+Z) 61 23.462 >Basic (H+K+R) 35 13.462 >Acidic (B+D+E+Z) 26 10.000 > >Created phikz-lys-pep.octanol.1.png
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bug 153766
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101091
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101225
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