1.4.2 Correspondence Analysis of Codon Usage J. Peden codonw codonw perl "codonw -silent -nomenu -nowarn" 0 outfiles perl " $seqfile.indices $seqfile.bulk" 2000 results_files *.indices *.bulk seqfile Sequences File perl " $value" 1000 8 defaults Defaults settings gc Genetic codes perl ($value && $value ne $vdef)? " -code $value" : "" 0 2 0 (0) Universal Genetic code [TGA=* TAA=* TAG=*] 1 (1) Vertebrate Mitochondrial code [AGR=* ATA=M TGA=W] 2 (2) Yeast Mitochondrial code [CTN=* ATA=M TGA=W] 3 (3) Filamentous fungi Mitochondrial code [TGA=W] 4 (4) Insects and Plathyhelminthes Mitochondrial co [ATA=M TGA=W AGR=S] 5 (5) Nuclear code of Cilitia [UAA=Q=Gln UAG=Q] 6 (6) Nuclear code of Euplotes [UGA=C] 7 (7) Mitochondrial code of Echinoderms UGA=W AGR=S AAA=N fop_values Fop/CBI values perl ($value)? " -f_type $value" : "" 0 2 0 (0) Escherichia coli 1 (1) Bacillus subtilis 2 (2) Dictyostelium discoideum 3 (3) Aspergillus nidulans 4 (4) Saccharomyces cerevisiae 5 (5) Drosophila melanogaster 6 (6) Caenorhabditis elegans 7 (7) Neurospora crassa cai_values CAI values perl ($value)? " -c_type $value" : "" 0 2 0 (0) Escherichia coli 1 (1) Bacillus subtilis 2 (2) Saccharomyces cerevisiae output_type Output Computer readable perl ($value)? " -machine" : "" 0 2 genes Concatenate genes (instead of individual genes) perl ($value)? " -totals" : "" 3 CU_options Codon usage indices CAI Codon Adaptation Index (CAI) perl ($value)? " -cai" : "" 4 perl ! $all_indices Fop Frequency of OPtimal codons (Fop) perl ($value)? " -fop" : "" 4 perl ! $all_indices CBI Codon bias index (CBI) perl ($value)? " -cbi" : "" 4 perl ! $all_indices cai_file User input file of CAI values (may be computed by a previous COA) perl ($value)? " -cai_file $value" : "" 2 perl $CAI codonw_coa_file perl 1 fop_file User input file of Fop values (may be computed by a previous COA) perl ($value)? " -fop_file $value" : "" 2 perl $Fop cbi_file User input file of CBI values (may be computed by a previous COA) perl ($value)? " -cbi_file $value" : "" 2 perl $CBI ENc Effective Number of Codons (ENc) perl ($value)? " -enc" : "" 4 perl ! $all_indices GC GC content of gene (G+C) perl ($value)? " -gc" : "" 4 perl ! $all_indices GC3s GC of silent 3rd codon posit. (GC3s) perl ($value)? " -gc3s" : "" 4 perl ! $all_indices silent_bc Silent base composition perl ($value)? " -sil_base" : "" 4 perl ! $all_indices all_indices All the above indices perl ($value)? " -all_indices" : "" 4 L_sym Number of synonymous codons (L_sym) perl (defined $value)? " -L_sym" : "" 4 L_aa Total Number of synonymous and non-synonymous codons (L_aa) perl ($value)? " -L_aa" : "" 4 Hydro Hydrophobicity of protein (Hydro) perl ($value)? " -hyd" : "" 4 Aromo Aromaticity of protein (Aromo) perl ($value)? " -aro" : "" 4 bulk_output_option Other output option perl ($value && $value ne $vdef)? " $value" : "" -cu 4 -cu Codon Usage (CU) -aau Amino Acid Usage (AAU) -raau Relative Amino Acid Usage (RAAU) -cutab Tabulation of codon usage -cutot Tabulation of dataset's codon usage -rscu Relative Synonymous Codon Usage (RSCU) -fasta fasta format -reader Reader format (codons are seperated by spaces) -transl Conceptual translation of DNA to amino acid -base Detailed report of codon G+C composition -dinuc Dinucleotide usage of the three codon pos. -noblk No bulk output to be written to file COA_options Correspondence analysis options (available for several sequences) coa_cu COA on codon usage perl ($value)? " -coa_cu" : "" 3 coa_rscu COA on RSCU perl ($value)? " -coa_rscu" : "" 3 coa_aa COA on Amino Acid usage perl ($value)? " -coa_aa" : "" 3 coa_expert Generate detailed(expert) statistics on COA perl ($value)? " -coa_expert" : "" 3 coa_axes Select number of axis to record perl (defined $value)? " -coa_axes $value" : "" 3 coa_num Select number of genes to use to identify optimal codons perl (defined $value)? " -coa_num $value" : "" 3 Values can be whole numbers or a percentage (5 or 10%). cai_coa perl "" "cai.coa" 1 codonw_coa_file perl 1 coa_files perl $coa_cu || $coa_rscu || $coa_aa *.coa coa_raw