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Revision 87 - (hide annotations)
Fri Dec 21 18:14:12 2018 UTC (4 months, 4 weeks ago) by aloraine
File size: 8823 byte(s)
Add zebrafish May 2017 genome and annotations
1 aloraine 66 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 aloraine 87 AddDescription "Danio rerio (May 2017) zebrafish (GRCz11/danRer11)" D_rerio_May_2017
60 aloraine 66 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 aloraine 84 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 aloraine 66 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 aloraine 85 AddDescription "Bos taurus (Jun 2014) cow (UMD_3.1.1/bosTau8)" B_taurus_Jun_2014
93 aloraine 66 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 aloraine 77 AddDescription "Mus musculus (Aug 2005) mouse (NCBI35/mm7)" M_musculus_Aug_2005
109 aloraine 66 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 aloraine 83 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 aloraine 66 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 aloraine 84 AddDescription "Solanum tuberosum Group Phureja clone DM1-3 (potato) v4.03" S_tuberosum_DM_Jul_2011
123 aloraine 66 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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