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Revision 87 - (show annotations)
Fri Dec 21 18:14:12 2018 UTC (2 months ago) by aloraine
File size: 8823 byte(s)
Add zebrafish May 2017 genome and annotations
1 Options +Indexes
2 IndexOptions FancyIndexing HTMLTable SuppressRules
3 IndexOptions IconsAreLinks ScanHTMLTitles NameWidth=* DescriptionWidth=*
4
5 # Autoindex-Strapdown Directives
6 AddType text/plain .md
7 HeaderName HEADER.md
8 ReadmeName README.md
9
10 # Customize by setting theme and title
11 IndexHeadInsert "<script>conf = {theme: 'united', title: 'Integrated Genome Browser QuickLoad Site'};</script> \
12 strapdown: '/styling/strapdown/v/0.2/strapdown.js'};</script> \
13 <script src='/styling/autoindex_strapdown.js'></script> \
14 <link rel='stylesheet' href='/styling/autoindex_strapdown.css'>"
15
16 # Icons using Bootstrap's Glyphicon set
17 DefaultIcon /styling/icons/glyphicon-file.svg
18 AddIcon /styling/icons/blank.svg ^^BLANKICON^^
19 AddIcon /styling/icons/glyphicon-folder-open.svg ^^DIRECTORY^^
20 AddIcon /styling/icons/glyphicon-circle-arrow-up.svg ..
21 AddIconByType (TXT,/styling/icons/glyphicon-file.svg) text/*
22 AddIconByType (IMG,/styling/icons/glyphicon-picture.svg) image/*
23 AddIconByType (SND,/styling/icons/glyphicon-music.svg) audio/*
24 AddIconByType (VID,/styling/icons/glyphicon-film.svg) video/*
25
26 IndexIgnore HEADER* README* FOOTER* /styling *~ *#
27 AddDescription "Tells search engines what to ignore" robots.txt
28 AddDescription "Taxonomic and common names for species, shown in IGB species menu" species.txt
29 AddDescription "Chromosome synonyms" chromosome.txt
30 AddDescription "Lists size of largest transcript, for RNA-Seq normalization" tx_sizes.txt.gz
31 AddDescription "Icon IGB displays for this data source in the Data Access tab" favicon.ico
32 AddDescription "Sequence data in blat 2bit format" *.2bit
33 AddDescription "Sequence data in fastq format" *.fastq.gz
34 AddDescription "BedGraph (wiggle) format file" *.wig.gz
35 AddDescription "BedGraph (wiggle) format file" *.bedgraph.gz
36 AddDescription "Cytobands file" cytoBand.cyt
37 AddDescription "Tabix index file" *.gz.tbi
38 AddDescription "PSL (alignments) blat output file" *.psl.gz
39 AddDescription "Loraine Lab FindJunctions file" *.FJ.bed.gz
40 AddDescription "Data from UCSC refGene table" *_refGene.bed.gz
41 AddDescription "Annotation or junction file" *.bed.gz
42 AddDescription "Annotation or junction file" *.bed
43 AddDescription "EST alignments" EST
44 AddDescription "mRNA alignments" mRNA
45 AddDescription "Anopheles gambiae (Feb 2003) mosquito (anoGam1/IAGP v.MOZ2)" A_gambiae_Feb_2003
46 AddDescription "Ailuropoda melanoleuca (Dec 2009) giant panda (ailMel1/BGI-Shenzhen AilMel 1.0)" A_melanoleuca_Dec_2009
47 AddDescription "Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 )" A_mellifera_Jan_2005
48 AddDescription "Arabidopsis thaliana TAIR9, TAIR10 genome assembly" A_thaliana_Jun_2009
49 AddDescription "Arabidopsis thaliana TAIR8 genome assembly" A_thaliana_Apr_2008
50 AddDescription "Arabidopsis thaliana TIGR5 genome assembly" A_thaliana_Jan_2004
51 AddDescription "Slime mold" D_discoideum
52 AddDescription "Medicago truncatula" M_truncatula_Mar_2009
53 AddDescription "Castor bean" R_communis
54 AddDescription "Arabidopsis lyrata JGI v1.0 assembly" A_lyrata_Apr_2011
55 AddDescription "Escherichia coli K12-MG1655" E_coli_K12-MG1655_Jan_2012
56 AddDescription "Fragaria vesca (woodland strawberry) v1.1" F_vesca_Sep_2011
57 AddDescription "Cavia porcellus (Feb 2008) guinea pig (cavPor3)" C_porcellus_Feb_2008
58 AddDescription "C. elegans Oct 2010 (WS220/ce10)" C_elegans_Oct_2010
59 AddDescription "Danio rerio (May 2017) zebrafish (GRCz11/danRer11)" D_rerio_May_2017
60 AddDescription "Danio rerio (Jul 2010) zebrafish (danRer7/Zv9)" D_rerio_Jul_2010
61 AddDescription "Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5)" D_melanogaster_Apr_2006
62 AddDescription "Drosophila melanogaster (July 2014) fruit fly (dmel_r6.03_FB2014_06)" D_melanogaster_Jul_2014
63 AddDescription "Equus caballus (Sep 2007) horse (equCab2)" E_caballus_Sep_2007
64 AddDescription "Felis catus (Dec 2008) cat (NHGRI/GTB V17e/felCat4)" F_catus_Dec_2008
65 AddDescription "Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0)" G_gallus_Nov_2011
66 AddDescription "Loxodonta africana (Jul 2009) elephant (loxAfr3)" L_africana_Jul_2009
67 AddDescription "Papaya" C_papaya_Aug_2010
68 AddDescription "Brachypodium distachyon (a model grass) JGI v1.0 8x assembly" B_distachyon_Aug_2010
69 AddDescription "Homo sapiens hg38 (Genome Reference Consortium GRCh38)" H_sapiens_Dec_2013
70 AddDescription "Homo sapiens hg19 (Genome Reference Consortium GRCh37)" H_sapiens_Feb_2009
71 AddDescription "Homo sapiens hg18 (Genome Reference Consortium GRCh36)" H_sapiens_Mar_2006
72 AddDescription "Homo sapiens hg17 (Genome Reference Consortium GRCh35)" H_sapiens_May_2004
73 AddDescription "Nematostella vectensis, starlet sea anemone" N_vectensis_Jun_2007
74 AddDescription "Chlamy (an algal genome)" C_reinhardtii_Nov_2010
75 AddDescription "Camelina, false flax, an oilseed crop" C_sativa_DH55_Apr_2014
76 AddDescription "Rice, japonic variety" O_sativa_japonica_Jun_2009
77 AddDescription "Rice, japonic variety Os-Nipponbare-Reference-IRGSP-1.0 assembly" O_sativa_japonica_Oct_2011
78 AddDescription "Soybean Glyma1" G_max_Aug_2010
79 AddDescription "Soybean Glyma2" G_max_Jan_2014
80 AddDescription "S. cerevisiae strain S288C (Apr 2011) budding yeast (sacCer3)" S_cerevisiae_Apr_2011
81 AddDescription "S. cerevisiae strain S288C (Jun 2008) budding yeast (sacCer2)" S_cerevisiae_Jun_2008
82 AddDescription "Fission yeast" S_pombe_Aug_2007
83 AddDescription "Volvox" V_carteri_Jul_2010
84 AddDescription "Wine grape 12x assembly" V_vinifera_Mar_2010
85 AddDescription "Physcomitrella patens (moss)" P_patens_Jan_2008
86 AddDescription "Black cottonwood (poplar)" P_trichocarpa_Aug_2012
87 AddDescription "Black cottonwood (poplar)" P_trichocarpa_Jan_2010
88 AddDescription "Sorghum bicolor" S_bicolor_Jan_2009
89 AddDescription "Sorghum bicolor" S_bicolor_Jun_2013
90 AddDescription "Candida albicans" C_albicans
91 AddDescription "Zea mays B73 RefGen_v2 assembly" Z_mays_B73_Mar_2010
92 AddDescription "Bos taurus (Jun 2014) cow (UMD_3.1.1/bosTau8)" B_taurus_Jun_2014
93 AddDescription "Bos taurus (cow) bosTau7 Oct 2011 assembly" B_taurus_Oct_2011
94 AddDescription "C. elegans May 2008 WS190/ce6" C_elegans_May_2008
95 AddDescription "Annotation and data file list" annots.[txt|xml]
96 AddDescription "Chromosome lengths and assembly information" mod_chromInfo.txt
97 AddDescription "Chromosome lengths and assembly information" genome.txt
98 AddDescription "IGB synonym file" synonyms.txt
99 AddDescription "Available genome assemblies and their titles" contents.txt
100 AddDescription "Mitochondrial Genome (Fasta format)" [Cc]hrM.fa*
101 AddDescription "Chloroplast Genome (Fasta format)" [Cc]hrC.fa*
102 AddDescription "Peach v1 genome assembly" P_persica_Apr_2010
103 AddDescription "Thermococcus kodakaraensis" T_kodakaraensis_KOD1_May_2004
104 AddDescription "Xenopus tropicalis JGI 4.2/xenTro3" X_tropicalis_Nov_2009
105 AddDescription "Mus musculus (Dec 2011) mouse (GRCm38/mm10)" M_musculus_Dec_2011
106 AddDescription "Mus musculus (Jul 2007) mouse (NCBI37/mm9)" M_musculus_Jul_2007
107 AddDescription "Mus musculus (Feb 2006) mouse (NCBI36/mm8)" M_musculus_Feb_2006
108 AddDescription "Mus musculus (Aug 2005) mouse (NCBI35/mm7)" M_musculus_Aug_2005
109 AddDescription "Malus domestica (Jun 2017) apple" M_domestica_Borkh_Jun_2017
110 AddDescription "Musa acuminata DH Pahang (Jan 2016) banana (v2)" M_acuminata_DH_Pahang_Jan_2016
111 AddDescription "Pan troglodytes (Oct 2010) chimpanzee (CGSC 2.1.3/panTro3)" P_troglodytes_Oct_2010
112 AddDescription "Ovis aries (Feb 2010) sheep (ISGC Ovis_aries_1/oviAri1)" O_aries_Feb_2010
113 AddDescription "Rattus norvegicus (Jul 2014) rat (RGSC 6.0/rn6)" R_norvegicus_Jul_2014
114 AddDescription "Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5)" R_norvegicus_Mar_2012
115 AddDescription "Solanum lycopersicum (Feb 2017) tomato (SL3.0)" S_lycopersicum_Feb_2017
116 AddDescription "Solanum lycopersicum (Feb 2014) tomato (SL2.50)" S_lycopersicum_Feb_2014
117 AddDescription "Solanum lycopersicum (May 2012) tomato (SL2.40)" S_lycopersicum_May_2012
118 AddDescription "S. pombe (May 2012) fission yeast" S_pombe_May_2012
119 AddDescription "Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3)" T_rubripes_Oct_2011
120 AddDescription "Thellungiella parvula (salt cress) v2, May 2012" T_parvula_May_2012
121 AddDescription "Felis catus (Sep 2011) cat (ICGSC Felis_catus 6.2/felCat5)" F_catus_Sep_2011
122 AddDescription "Solanum tuberosum Group Phureja clone DM1-3 (potato) v4.03" S_tuberosum_DM_Jul_2011
123 AddDescription "Tribolium castaneum (March 2008) red flour beetle" T_castaneum_Mar_2008
124 AddDescription "Lotmaria passim, strain SF, Crithidia mellificae strain SF, whole genome shotgun sequencing project" L_passim_Apr_2014
125 AddDescription "Yarrowia lipolytica CLIB122 (Jul 2004) Assembly GCA_000002525.2" Y_lipolytica_CLIB122_Jul_2004
126 AddDescription "Yarrowia lipolytica PO1f (May 2014) Assembly GCA_000590845.2" Y_lipolytica_PO1f_May_2014
127 AddDescription "Yarrowia lipolytica WSH-Z06 (Mar 2014) Assembly GCA_000613155.1" Y_lipolytica_WSH-Z06_Mar_2014

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