GeneMark 2.4b locate genes within a DNA sequence Borodovsky, McIninch Borodovsky, M., Sprizhitsky Yu, Golovanov E. and Alexandrov A. (1986) Statistical Patterns in Primary Structures of Functional Regions in the E. Coli Genome: II. Non-homogeneous Markov Models. Molecular Biology, 20, 833-840. Borodovsky, M., Sprizhitsky Yu., Golovanov E. and Alexandrov A. (1986) Statistical Patterns in Primary Structures of Functional Regions in the E. Coli Genome: III. Computer Recognition of Coding Regions. Molecular Biology, 20, 1145-1150. Borodovsky, M. and McIninch J. (1993) GENMARK: Parallel Gene Recognition for both DNA Strands. Computers and Chemistry, 17, 123-133. nucleic:translation gene finding genemark genemark perl "gm" 0 outfiles *.lst *.ldata *.gdata *.ps *.rgn *.orf *.bla *.fas seq Sequence File perl " $value" 100 matrix Matrix, according to specie (-m) perl ($value)? " -m $value" : "" 2 A.thaliana_1_4.mat A.thaliana_2_4.mat at_hi_3.mat at_lo_3.mat ahv1_3.mat arthro2.mat C.trachomatis_4.mat bjaponicum_3.mat burgdorferi_4.mat c.trachomatis_4.mat capri_4.mat capsulatus_2.mat ce_hi_3.mat ce_lo_3.mat chlamy.highGC_4.mat chlamy.highgc_4.mat chlamy_4.mat dm_hi_4.mat dm_lo_4.mat ebv_2.mat ec_hiexp_3.mat ec_phage_3.mat ecoli_4.mat ecoli_5.mat ehv2_2.mat fugu_2.mat genit_2.mat gg_hi_4.mat gg_lo_4.mat giardia2.mat gono_3.mat hcmv_2.mat hhv8_3.mat hinflu_4.mat hum_23_4.mat hum_49_4.mat hum_55_4.mat hum_79_4.mat hum_hi_4.mat hum_lo_4.mat jann_4.mat kpneu_3.mat lacto2.mat lep_3.mat lp_hi_2.mat lp_lo_2.mat mm_hi_4.mat mm_lo_4.mat mpneu_4.mat myco_3.mat P.aeruginosa_3.mat P.furiosus_2.mat p.aeruginosa_3.mat p.furiosus_2.mat pallidum_4.mat phi80m3_2.mat prowazekii_4.mat pylori_2.mat pyogenes_3.mat radiodurans_4.mat rhizo.leg_3.mat rhizo.mel_4.mat rice_3.mat rn_hi_4.mat rn_lo_4.mat rubella_2.mat s.cerevisiae_at_3.mat s.cerevisiae_t_5.mat S.cerevisiae_AT_3.mat S.cerevisiae_T_5.mat sc_hi_4.mat sc_lo_4.mat saimiri_2.mat salm_4.mat saureus_3.mat solf_2.mat sp_hi_3.mat sp_lo_3.mat strepneu_2.mat subt_4.mat syn_4.mat t4_3.mat thalian4.mat theil_3.mat thermo_4.mat tuber_4.mat volvox_2.mat x_hi_3.mat x_lo_3.mat yeast_5.mat 933wv4_2.mat All the package proposed matrices are given here, which is a lot! You can choose it according to the organism. The last number given in the name is the order of the IMM (Interpolated Markov Chain): the bigger, the more complete/complex. _hi_ indicates high GC content, _lo_ indicates low GC content, ... and the standard error file gives sometimes a complete name of the matrix. search Search parameters 2 threshold Probability threshold to identify gene-encoding ORFs (-t) perl ($value && $value != $vdef)? " -t $value" : "" 0.5 2 step Step size (-s) perl ($value && $value != $vdef)? " -s $value" : "" 12 2 Step the coding evaluation window step-size nucleotides for each evaluation. This parameter does not affect prediction performance so long as it is kept small (the default is 12). This value does, however, affect the number of data points in the graphical output and, hence, the size of the associated postscript file. window Size of the sliding evaluation window (-w) perl ($value && $value != $vdef)? " -w $value" : "" 96 2 Use a sliding evaluation window of window-size nucleotides. The default value is 96. Smaller values may find smaller (< window-size nucleotides) coding fragments, but prediction accuracy will decrease. Large values will yield stronger signals for large open-reading frames but skip over smaller coding fragments. codon Codon table (-c) perl ($value)?" -c $value":"" 2 If specified, gm reads the file codon-table for a list of alternate codon translations. The codon-table file has a simple format: the codon is listed and followed by either a single letter IUPAC symbol for it's amino acid translation, the word 'start' to indicate it is a start codon, the word 'rare' to indicate is is a rare start codon, or the word 'stop' (or '*') to indicate the codon is a termination codon. The file should contain one codon per line and only those codons that differ from the standard encoding need to be listed. output_options Output options 3 list_options List options (-l) 3 perl ($list_off || $list_orf || $list_regions || $list_exons || $list_quiet)? " -l$list_off$list_orf$list_regions$list_exons$list_quiet" : "" list_off Turn all options off (0) perl ($value && ($list_off=0))? "" : "" list_orf List open reading frame predictions (o) perl ($value && ($list_orf="o"))? "" : "" Includes RBS evaluations, if applicable. list_regions List regions (r) perl ($value && ($list_regions="r"))? "" : "" List regions (from termination-codon to termination-codon in the same reading frame) that have a strong local signal in side of them. list_exons List possible exons (x) perl ($value && ($list_exons="x"))? "" :"" List possible exons (signals not correlated with a particular open reading frame). list_quiet Quiet. Disable the file header information (q) perl ($value && ($list_quiet="q"))? "" :"" do_postscript Graphical output in PostScript perl ($value)? " -g$graph_off$graph_orf$graph_regions$graph_exons$frameshift$scale$landscape$termination$start" : "" 1 5 graph_options Graphical output options (-g) perl $do_postscript 4 zoom Zoom level (-z) perl (defined $value)?" -z $value":"" 4 The number of nucleotides appearing on each page in the graphical output is multiplied by zoom-level. perl $do_postscript graph_off Turn all options off (0) perl ($value && ($graph_off=0))? "" : "" 4 perl $do_postscript graph_orf Indicate open reading frames with a horizontal line at the 0.5 level (o) perl ($value && ($graph_orf="o"))? "" : "" 4 perl $do_postscript graph_regions Indicate regions with grey bars at the 0.35 level (r) perl ($value && ($graph_regions="r"))? "" : "" 4 indicate regions (from termination-codon to termination-codon in the same reading frame) that have a strong local signal in side of them. perl $do_postscript graph_exons Indicate possible exons (x) perl ($value && ($graph_exons="x"))? "" :"" 4 Indicate possible exons (signals not correlated with a particular open reading frame). perl $do_postscript frameshift Indicate suspected frameshift errors (f) perl ($value && ($frameshift="f"))? "" :"" 4 Indicate suspected frameshift errors (indicated by a sudden change in signal frame). perl $do_postscript scale Use an alternative horizontal scale based on powers of 10 (k) perl ($value && ($scale="k"))? "" :"" 4 perl $do_postscript landscape Landscape output (l) perl ($value && ($landscape="l"))? "" :"" 4 perl $do_postscript termination Indicate termination codons with a vertical tick (n) perl ($value && ($termination="n"))? "" :"" 4 Indicate termination codons with a vertical tick extending downward from the 0.5 level. perl $do_postscript start Indicate start and rare start codons with a vertical tick (s) perl ($value && ($start="s"))? "" :"" 4 Indicate start and rare start codons with vertical ticks extending from the 0.5 level. perl $do_postscript region_options Regions output options (-r) 5 perl ($region_off || $region_translation || $region_nucleotide || $region_quiet)? " -r$region_off$region_translation$region_nucleotide$region_quiet" : "" region_off Turn all options off (0) perl ($value && ($region_off=0))? "" : "" 4 region_translation Write amino acid translations of the indicated regions (p) perl ($value && ($region_translation="p"))? "" : "" 4 region_nucleotide Write a copy of the nucleotide sequence of the indicated regions (n) perl ($value && ($region_nucleotide="n"))? "" : "" 4 region_quiet Suppress header information in the generated file. (q) perl ($value && ($region_quiet="q"))? "" :"" 4 orf_options ORF output options (-o) 5 perl ($orf_off || $orf_translation || $orf_nucleotide || $orf_quiet)? " -o$orf_off$orf_translation$orf_nucleotide$orf_quiet" : "" orf_off Turn all options off (0) perl ($value && ($orf_off=0))? "" : "" 4 orf_translation Write amino acid translations of the indicated ORF (p) perl ($value && ($orf_translation="p"))? "" : "" 4 orf_nucleotide Write a copy of the nucleotide sequence of the indicated ORF (n) perl ($value && ($orf_nucleotide="n"))? "" : "" 4 orf_quiet Suppress header information in the generated file. (q) perl ($value && ($orf_quiet="q"))? "" :"" 4