SPACne Identification of polypeptides using their amino-acid composition Antonini F., Gaillard S., Grillasca JP. S. Gaillard, F. Antonini, N. Joly, J.N. Gouze and J.P. Grillasca. Sequence Protein Alignement with Composition New Evolutions (SPACne): A program for the identification of polypeptides using amino acid composition. 2004. Cell. Mol. Biol. 50(7), 801-803. protein:composition spacne spacne perl "spacne < params && spacne_html.pl result.txt > result.html" params perl "composition.txt\ntrisol.txt\nanalysis.txt\nresult.txt\n" params -1 composition Composition name Name of composition perl "$value\n" 50 composition.txt it is optional. weight Weight (Daltons) perl "$value\n" 51 composition.txt in Dalton, it is an obligatory parameter. comment Comment perl "$value\n" 52 composition.txt it is optional. alxglx Use Asx and Glx perl (defined $value) ? "$value\n" : "0\n" 53 composition.txt This option allows the user to take into account two \"summed up\" residues, Asx (Asp and Asn) and Glx (Glu and Gln). cystrp Do not count Cys and Trp perl (defined $value) ? "$value\n" : "0\n" 54 composition.txt In some experimental conditions, these two amino acids are destroyed. Algorithm eliminate the contribution of Cys and Trp residues in matching sequence although this residues are still taken into account in the MW determination. ala Ala (A) perl (defined $value) ? "$value\n" : "0\n" 75 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) asx Asx (B) perl (defined $value) ? "$value\n" : "0\n" 76 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) cys Cys (C) perl (defined $value) ? "$value\n" : "0\n" 77 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) asp Asp (D) perl (defined $value) ? "$value\n" : "0\n" 78 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) glu Glu (E) perl (defined $value) ? "$value\n" : "0\n" 79 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) phe Phe (F) perl (defined $value) ? "$value\n" : "0\n" 80 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) gly Gly (G) perl (defined $value) ? "$value\n" : "0\n" 81 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) his His (H) perl (defined $value) ? "$value\n" : "0\n" 82 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) ile Ile (I) perl (defined $value) ? "$value\n" : "0\n" 83 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) lys Lys (K) perl (defined $value) ? "$value\n" : "0\n" 85 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) leu Leu (L) perl (defined $value) ? "$value\n" : "0\n" 86 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) met Met (M) perl (defined $value) ? "$value\n" : "0\n" 87 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) asn Asn (N) perl (defined $value) ? "$value\n" : "0\n" 88 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) pro Pro (P) perl (defined $value) ? "$value\n" : "0\n" 90 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) gln Gln (Q) perl (defined $value) ? "$value\n" : "0\n" 91 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) arg Arg (R) perl (defined $value) ? "$value\n" : "0\n" 92 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) ser Ser (S) perl (defined $value) ? "$value\n" : "0\n" 93 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) thr Thr (T) perl (defined $value) ? "$value\n" : "0\n" 94 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) val Val (V) perl (defined $value) ? "$value\n" : "0\n" 96 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) trp Trp (W) perl (defined $value) ? "$value\n" : "0\n" 97 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) tyr Tyr (Y) perl (defined $value) ? "$value\n" : "0\n" 99 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) glx Glx (Z) perl (defined $value) ? "$value\n" : "0\n" 100 composition.txt Percent must be in [0.0,100.0] interval perl ($value < 0.0 or $value > 100.0) end_compo perl "//\n" 101 composition.txt analysis Analysis options bank_name Sequence databank uniprot genbank_rel genbank_est genbank_gss genbank_htg uniprot perl "/local/gensoft/share/spacne/$value\n" The choice is UniProt or Genbank for the DNA. The DNA sequences are translated into the 6 reading frame before the analysis. params bank_type perl ($bank_name =~ /^uniprot/) ? "1\n0\n" : "0\n1\n" 10 analysis.txt superkingdom Super-Kingdom perl "$value\n" All Archaea Bacteria Eubacteria Eukaryota Viroids Viruses Others All 11 analysis.txt This option limits the research at one Super-kingdom: Archaea, Eubacteria, Eukaryota, Viroids, Viruses and the other. genus Genus name (example: Homo, Arabidopsis, Escherichia or Rattus) perl (defined $value) ? "$value\n" : "All\n" "" 12 analysis.txt This option limits the research at one Genus. minweight Percent mini of weight (%) perl "$value\n" 13 analysis.txt 10.0 when the apparent MW is entered, percentage variation in plus or minus can be separately specified. maxweight Percent maxi of weight (%) perl "$value\n" 14 analysis.txt 10.0 when the apparent MW is entered, percentage variation in plus or minus can be separately specified. indexdiff Index difference to keep (%) perl "$value\n" 15 analysis.txt 5.0 the DI threshold may be specified before the launching, or considered as 5 by default. nbsol Number of solutions perl "$value\n" 16 analysis.txt 100 This number gives the maximum number of solutions that SPAC retrieved. end_analysis perl "//\n" 17 analysis.txt output Output sort Sort output by id sk ge id "1\n0\n0\n" sk "0\n1\n0\n" ge "0\n0\n1\n" id 200 trisol.txt Index difference : The solutions are arranged according to their DI by increasing order. Super-Kingdom : The solutions are sorted out by super-kingdom and according to their ID. Genus name : The solutions are listed by super-kingdom, by kind and according to their ID. result result.txt result.html