## ## ISMB_a4.rc ## ## This is the gff2ps configuration file ## for the ISMB99 ADH poster: ## "The challenge of annotating a complete eukaryotic genome" ## ## $Id: ISMB_a4.rc,v 1.1 2000/01/10 21:34:10 jabril Exp jabril $ # # L ######PAGE LAYOUT & PROGRAM OPTIONS###### # margin_upper=1cm margin_bottom=1cm margin_right=1cm margin_left=1cm background_color=white foreground_color=black # # We must define this zoom because there is one GFF-record # starting at -1 (???), which moves nucleotide origin to -100 on axes. zoom=0..* # block_style=default show_blocks_top-bottom=1 default_block_spacing_width=0.25cm default_track_width=1cm default_track_spacing_width=0.25cm strand_show_forward=on strand_show_independent=on strand_show_reverse=on default_scale_width=0.25cm major_tickmarks_nucleotides=25000 # major_tickmarks_num=10 # minor_tickmarks_nucleotides=-1 minor_tickmarks_num=25 show_positions=false # # frame0_color=blue # frame1_color=red # frame2_color=green # frame_unknown_color=orange # header_style=boxed title=The Challenge of Annotating a Complete Eukaryotic Genome subtitle=A case of study in Drosophila melanogaster: 2.9 Mb from Adh region on chromosome 3. show_page_numbers=on show_time=off show_date=off # left_source_label_width=3cm # # # G ############GROUP FEATURES############ # # For All Groups !/.*ID_(Fou|G\+C).*/::group_shape=line *::group_line=bracket # /.*std.*/::group_line_color=black # ############### A # /.*GeneWise.*/::group_line_color=darkskyblue /.*GeneMarkHMM.*/::group_line_color=seagreen /.*MAGPIE.*/::group_line_color=violet /.*GeneID.*/::group_line_color=darkorange /.*BLOCKS.*/::group_line_color=darkgreen /.*HMMGene.*/::group_line_color=darkred /.*grailexp.*/::group_line_color=brown /.*Genie.*/::group_line_color=magenta /.*FGenes.*/::group_line_color=limegreen # ############### B # /.*MAGPIEProm.*/::group_line_color=darkcyan /.*LME.*/::group_line_color=darkcyan /.*GenieProm.*/::group_line_color=darkcyan /.*CoreInspector.*/::group_line_color=darkcyan # ############### C # /.*TRF.*/::group_line_color=blue /.*Calypso.*/::group_line_color=blue # # # S ############SOURCE FEATURES############ # # Data-Sets for Adh region from BDGP std1::left_label=ADH - Std1 std3::left_label=ADH - Std3 /std.*/::group_color=grey /std.*/::feature_color=yellow /std.*/::source_line_color=black # # Whole Sequence Analysis. GeneID_Fou::left_label=Fourier Analysis GeneID_Fou::source_line=none GeneID_G+C::left_label=G+C Content GeneID_G+C::source_line=none # ############### A # # Birney - GeneWise GeneWise::left_label=GeneWise GeneWise::feature_color=lightskyblue GeneWise::group_color=darkskyblue GeneWise::source_line_color=darkskyblue # # Borodovsky - GeneMark.hmm GeneMarkHMM::left_label=GeneMark HMM GeneMarkHMM::feature_color=lightseagreen GeneMarkHMM::group_color=seagreen GeneMarkHMM::source_line_color=seagreen # # Gaasterland - MAGPIE, repeats & promoters MAGPIE::left_label=MAGPIE MAGPIEexon::left_label=MAGPIE (Exons) /MAGPIE(exon)?/::feature_color=lightviolet /MAGPIE(exon)?/::group_color=violet /MAGPIE(exon)?/::source_line_color=violet # # Guigo - GeneID GeneID::left_label=GeneID GeneID::feature_color=lightorange GeneID::group_color=darkorange GeneID::source_line_color=darkorange # # Henikoff - BLOCKS BLOCKS::left_label=BLOCKS BLOCKS::feature_color=lightgreen BLOCKS::group_color=darkgreen BLOCKS::source_line_color=darkgreen # # Krogh - HMMGene HMMGene::left_label=HMMGene HMMGene::feature_color=verylightred HMMGene::group_color=darkred HMMGene::source_line_color=darkred # # Mural - GRAIL grailexp::left_label=GRAIL grailexp::feature_color=verylightbrown grailexp::group_color=brown grailexp::source_line_color=brown # # Reese - Genie, GenieEST and GenieESTHOM Genie::left_label=Genie GenieEST::left_label=Genie+EST GenieESTHOM::left_label=Genie+EST+HOM /Genie(EST(HOM)?)?/::feature_color=verylightmagenta /Genie(EST(HOM)?)?/::group_color=magenta /Genie(EST(HOM)?)?/::source_line_color=magenta # # Solovyev - CGG1, CGG2C and GG3 FGenesCGG1::left_label=FGenes (CGG1) FGenesCGG2::left_label=FGenes (CGG2) FGenesCGG3::left_label=FGenes (CGG3) /FGenes.*/::feature_color=lightlimegreen /FGenes.*/::group_color=limegreen /FGenes.*/::source_line_color=limegreen # ############### B # # Gaasterland - MAGPIE, repeats & promoters MAGPIEProm::left_label=MAGPIE-Promoters MAGPIEProm::feature_color=lightcyan MAGPIEProm::group_color=darkcyan MAGPIEProm::source_line_color=darkcyan MAGPIEProm::vert_align=baseline # # Reese - Genie, GenieEST and GenieESTHOM GenieProm::left_label=Genie-Promoters GenieProm::feature_color=lightcyan GenieProm::group_color=darkcyan GenieProm::source_line_color=darkcyan GenieProm::vert_align=baseline # # Ohler - LME_IMC and LME_SSM LMEIMC::left_label=LME-IMC TSS LMESSM::left_label=LME-SSM TSS /LME.*/::feature_color=lightcyan /LME.*/::group_color=darkcyan /LME.*/::source_line_color=darkcyan /LME.*/::vert_align=baseline # # Werner - CoreInspector CoreInspector::left_label=CoreInspector TSS CoreInspector::feature_color=lightcyan CoreInspector::group_color=darkcyan CoreInspector::source_line_color=darkcyan CoreInspector::vert_align=baseline # ############### C # # Gaasterland - MAGPIE, repeats & promoters calypso::left_label=MAGPIE (Calypso) calypso::feature_color=lightblue calypso::group_color=blue calypso::source_line_color=blue calypso::vert_align=center # # Benson - TandemRepeatFinder TRF::left_label=TandemRepeatFinder TRF::feature_color=lightblue TRF::group_color=blue TRF::source_line_color=blue TRF::vert_align=center # ############### # # # For All Sources *::unfold_grouped_ungrouped=off *::unfold_grouped_line=off *::unfold_ungrouped_line=off # # F ############GENOMIC FEATURES############ # ############### A # start_codon::shape=right_triangle start_codon::layer=20 CDS::shape=box CDS::layer=5 splice3::shape=up_triangle splice3::layer=20 exon::shape=box exon::layer=16 splice5::shape=down_triangle splice5::layer=20 stop_codon::shape=circle stop_codon::layer=20 # ############### B # promotor::shape=half_circle TSS::shape=half_diamond # ############### C # tandemrepeat::shape=circle tandem_repeat::shape=circle # ############### # # # For All Features *::fill_shape_mode=1_color *::fill_vector_mode=rainbow