Log of /quickload

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Revision 107 - Directory Listing
Modified Tue Sep 10 20:30:03 2019 UTC (5 years, 1 month ago) by aloraine

IGBF-1498 Add C. albicans Dec 2013 assembly and annotations

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Revision 106 - Directory Listing
Modified Tue Sep 10 20:25:45 2019 UTC (5 years, 1 month ago) by aloraine

Add American eel as per community request - see IGBF-1546

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Revision 105 - Directory Listing
Modified Tue Sep 10 20:21:38 2019 UTC (5 years, 1 month ago) by aloraine

Fix close tag

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Revision 104 - Directory Listing
Modified Tue Sep 10 20:21:08 2019 UTC (5 years, 1 month ago) by aloraine

Add Daphnia genomes

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Revision 103 - Directory Listing
Modified Tue Sep 10 20:20:25 2019 UTC (5 years, 1 month ago) by aloraine

Use tabix-indexed files for TAIR8 annotations

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Revision 102 - Directory Listing
Modified Tue Mar 26 16:43:52 2019 UTC (5 years, 6 months ago) by aloraine

Report sequences and sizes for patch 12

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Revision 101 - Directory Listing
Modified Tue Mar 26 16:43:30 2019 UTC (5 years, 6 months ago) by aloraine

Replace with http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/latest/hg38.p12.2bit (patch 12)

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Revision 100 - Directory Listing
Modified Sun Mar 24 18:58:05 2019 UTC (5 years, 6 months ago) by aloraine

Show SNPs with direction indicator none; use blue color for foreground

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Revision 99 - Directory Listing
Modified Sun Mar 24 18:37:02 2019 UTC (5 years, 6 months ago) by aloraine

Move RefSeq All to Genes and Gene Predictions folder because these have CDS annotations and are not simple alignments

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Revision 98 - Directory Listing
Modified Sun Mar 24 18:28:56 2019 UTC (5 years, 6 months ago) by aloraine

Highlight genetics data sets; Load RefSeq Curated as new reference gene models

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Revision 97 - Directory Listing
Modified Sun Mar 24 18:27:48 2019 UTC (5 years, 6 months ago) by aloraine

Update RefSeq alignment files; Add release 151 of dbSNP common SNPs

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Revision 96 - Directory Listing
Modified Sun Mar 24 15:58:56 2019 UTC (5 years, 6 months ago) by aloraine

Update 2019-03

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Revision 95 - Directory Listing
Modified Sun Mar 24 15:34:23 2019 UTC (5 years, 6 months ago) by aloraine

Update 2019-03

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Revision 94 - Directory Listing
Modified Mon Mar 18 23:13:38 2019 UTC (5 years, 6 months ago) by aloraine

Add green monkey sequence

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Revision 93 - Directory Listing
Modified Mon Mar 18 22:36:21 2019 UTC (5 years, 6 months ago) by aloraine

Describe Oct 2016 American eel, Oct 2006 mosquito, Mar 2014 green monkey, Dec 2013 Candida

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Revision 92 - Directory Listing
Modified Mon Mar 18 22:09:02 2019 UTC (5 years, 6 months ago) by aloraine

Add malaria mosquito Oct 2006 genome assembly and EnsGene annotations

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Revision 91 - Directory Listing
Modified Mon Mar 18 21:56:41 2019 UTC (5 years, 6 months ago) by aloraine

Add green monkey March 2014 assembly and annotations

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Revision 90 - Directory Listing
Modified Thu Jan 17 21:25:46 2019 UTC (5 years, 8 months ago) by aloraine

Add Candida albicans SC5314 Assembly 22 Jun_2014

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Revision 89 - Directory Listing
Modified Thu Jan 17 17:56:19 2019 UTC (5 years, 8 months ago) by aloraine

Add C. elegans Feb 2013 (WBcel235/ce11) genome assembly and gene models

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Revision 88 - Directory Listing
Modified Tue Jan 15 22:11:30 2019 UTC (5 years, 8 months ago) by aloraine

Add description for new genome versions ce11, chlSab2, C. albicans

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Revision 87 - Directory Listing
Modified Fri Dec 21 18:14:12 2018 UTC (5 years, 9 months ago) by aloraine

Add zebrafish May 2017 genome and annotations

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Revision 86 - Directory Listing
Modified Mon Dec 10 20:02:12 2018 UTC (5 years, 10 months ago) by aloraine

Add HEADER.md for rat & cow; Fix error

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Revision 85 - Directory Listing
Modified Mon Dec 10 19:58:13 2018 UTC (5 years, 10 months ago) by aloraine

Add bosTaur8 from UCSC Genome Bioinformatics

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Revision 84 - Directory Listing
Modified Wed Nov 7 23:17:59 2018 UTC (5 years, 11 months ago) by aloraine

Add description for potato, budding yeast, copied from contents.txt

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Revision 83 - Directory Listing
Modified Wed Nov 7 22:53:14 2018 UTC (5 years, 11 months ago) by aloraine

Add rat genome rn6

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Revision 82 - Directory Listing
Modified Mon Nov 5 23:25:44 2018 UTC (5 years, 11 months ago) by aloraine

Add rn6 (rat)

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Revision 81 - Directory Listing
Modified Sat Oct 27 01:49:24 2018 UTC (5 years, 11 months ago) by aloraine

Fix typos. Improve wording - make more succinct

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Revision 80 - Directory Listing
Modified Sat Oct 27 01:44:05 2018 UTC (5 years, 11 months ago) by aloraine

Remove broken link to UCSC downloads page (it moved)

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Revision 79 - Directory Listing
Modified Sat Oct 27 01:34:05 2018 UTC (5 years, 11 months ago) by aloraine

Fix typo; Suggest that psl files may not be available for every assembly

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Revision 78 - Directory Listing
Modified Sat Oct 27 01:26:56 2018 UTC (5 years, 11 months ago) by aloraine

Explain contents of newly added mm7 genome version directory

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Revision 77 - Directory Listing
Modified Sat Oct 27 01:22:16 2018 UTC (5 years, 11 months ago) by aloraine

Add M_musculus_Aug_2005Mus musculus (Aug 2005) mouse (NCBI35/mm7) assembly

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Revision 76 - Directory Listing
Modified Tue Oct 9 17:55:15 2018 UTC (6 years ago) by aloraine

Load Araport gene models instead of TAIR10 mRNA

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Revision 75 - Directory Listing
Modified Thu Oct 4 16:27:04 2018 UTC (6 years ago) by aloraine

Support potato genome

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Revision 74 - Directory Listing
Modified Thu Oct 4 16:26:23 2018 UTC (6 years ago) by aloraine

Add gene model annotations converted from http://solanaceae.plantbiology.msu.edu/data/PGSC_DM_V403_genes.gff.zip using gff3ToBedDetail.py from https://bitbucket.org/lorainelab/genomesource commit https://bitbucket.org/lorainelab/genomesource/commits/6ab3b3f9a0c903af27ff58a8347a86edc9a3b6af?at=master followed by sed command to change chromosome names from ST4.03chNN to chrNN to match genome sequence file

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Revision 73 - Directory Listing
Modified Thu Oct 4 16:20:24 2018 UTC (6 years ago) by aloraine

Add v4.03 July 2011 sequence for potato genome assembly

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Revision 72 - Directory Listing
Modified Thu Oct 4 16:17:53 2018 UTC (6 years ago) by aloraine

Remove Jan 2016 sequence, update chromosome listing file for Jul 2011 4.03 assembly, add annotations

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Revision 71 - Directory Listing
Modified Thu Oct 4 15:49:27 2018 UTC (6 years ago) by aloraine

Add potato version 4.03 genome assembly from https://www.nature.com/articles/nature10158 and http://solanaceae.plantbiology.msu.edu

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Revision 70 - Directory Listing
Modified Thu Oct 4 15:48:14 2018 UTC (6 years ago) by aloraine

Use version 4.03 released Jul 2011 instead

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Revision 69 - Directory Listing
Modified Thu Oct 4 15:18:06 2018 UTC (6 years ago) by aloraine

Fix typo; Version 4.03 not version 4.04

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Revision 68 - Directory Listing
Modified Wed Oct 3 15:02:04 2018 UTC (6 years ago) by aloraine

Adding potato v4.04 genome from SpudDB http://solanaceae.plantbiology.msu.edu

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Revision 67 - Directory Listing
Modified Thu Sep 27 22:00:02 2018 UTC (6 years ago) by aloraine

Add link to quickload repo in viewvc

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Revision 66 - Directory Listing
Modified Thu Sep 27 21:55:57 2018 UTC (6 years ago) by aloraine

Add configuration file for style; Assumes styling directory is in DocumentRoot

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Revision 65 - Directory Listing
Modified Thu Sep 27 17:07:58 2018 UTC (6 years ago) by aloraine

Add Lotmaria passim, strain SF, Crithidia mellificae strain SF, whole genome shotgun sequencing project, genome assembly and annotations (files by Nowlan Freese)

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Revision 64 - Directory Listing
Modified Thu Sep 27 17:02:57 2018 UTC (6 years ago) by aloraine

Add Zea Mays B73 RefGenv2 genome assembly and annotations, from Maize genome database

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Revision 63 - Directory Listing
Modified Thu Sep 27 16:57:14 2018 UTC (6 years ago) by aloraine

Add Y_lipolytica genomes, collected from Genbank

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Revision 62 - Directory Listing
Modified Thu Sep 27 16:53:23 2018 UTC (6 years ago) by aloraine

Add 12X March 2010 wine grape draft genome Vitis vinifera genome assembly

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Revision 61 - Directory Listing
Modified Thu Sep 27 16:46:52 2018 UTC (6 years ago) by aloraine

Add Volvox carteri f. nagariensis, Eve Jul 2010 assembly, collected from Phytozome

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Revision 60 - Directory Listing
Modified Thu Sep 27 16:44:53 2018 UTC (6 years ago) by aloraine

Add Thellungiella parvula (salt cress) v2, May 2012 genome assembly

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Revision 59 - Directory Listing
Modified Thu Sep 27 16:21:12 2018 UTC (6 years ago) by aloraine

Add Thermococcus kodakaraensis May 2004 genome, collected from Genbank accession NC_006624

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Revision 58 - Directory Listing
Modified Thu Sep 27 16:20:02 2018 UTC (6 years ago) by aloraine

Add Tribolium castaneum (March 2008) red flour beetle

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Revision 57 - Directory Listing
Modified Thu Sep 27 16:10:12 2018 UTC (6 years ago) by aloraine

Add S. pombe (May 2012) fission yeast genome assembly and annotations

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Revision 56 - Directory Listing
Modified Thu Sep 27 16:09:36 2018 UTC (6 years ago) by aloraine

Add Solanum lycopersicum (tomato) May 2012/SL2.40 genome assembly

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Revision 55 - Directory Listing
Modified Thu Sep 27 16:03:02 2018 UTC (6 years ago) by aloraine

Add Solanum lycopersicum (tomato) May 2012/SL2.40 and Feb 2014/SL2.50 genome assemblies and annotations

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Revision 54 - Directory Listing
Modified Thu Sep 27 15:59:21 2018 UTC (6 years ago) by aloraine

Add S. cerevisiae strain S288C (Apr 2011) budding yeast (sacCer3) genome assembly and annotations, collected from UCSC

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Revision 53 - Directory Listing
Modified Thu Sep 27 15:54:40 2018 UTC (6 years ago) by aloraine

Add Sorghum bicolor v1.0 and v2.0 (June 2013) genome assemblies, collected from Phytozome

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Revision 52 - Directory Listing
Modified Thu Sep 27 15:51:15 2018 UTC (6 years ago) by aloraine

Add Ricinis communis TIGR/JCVI v0.1 assembly, castor bean

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Revision 51 - Directory Listing
Modified Thu Sep 27 15:37:21 2018 UTC (6 years ago) by aloraine

Add JGI4.2/xenTro3 Xenopus tropicalis genome, Nov 2009 genome assembly and annotations, collected from UCSC

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Revision 50 - Directory Listing
Modified Thu Sep 27 15:35:20 2018 UTC (6 years ago) by aloraine

Add Rattus Norvegicus (Mar 2012) rat (RGSC 5.0/rn5) genome assembly collected from UCSC

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Revision 49 - Directory Listing
Modified Thu Sep 27 15:32:16 2018 UTC (6 years ago) by aloraine

Add Strapdown js and css files for more user-friendly look in Web browsers

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Revision 48 - Directory Listing
Modified Thu Sep 27 15:29:58 2018 UTC (6 years ago) by aloraine

Add Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3) genome assembly and annotations from UCSC

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Revision 47 - Directory Listing
Modified Thu Sep 27 15:28:01 2018 UTC (6 years ago) by aloraine

Add Pan troglodytes (Oct 2010) chimpanzee (CGSC 2.1.3/panTro3) collected from UCSC

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Revision 46 - Directory Listing
Modified Thu Sep 27 15:23:52 2018 UTC (6 years ago) by aloraine

Add Populus trichocarpa v2 and v3 genomes, collected from Phytozome

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Revision 45 - Directory Listing
Modified Thu Sep 27 15:21:28 2018 UTC (6 years ago) by aloraine

Add Prunus persica v1 genome assembly, collected from Phytozome v7

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Revision 44 - Directory Listing
Modified Thu Sep 27 15:19:32 2018 UTC (6 years ago) by aloraine

Add Physcomitrella patens Jan 2008 genome from CossMoss

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Revision 43 - Directory Listing
Modified Thu Sep 27 15:15:02 2018 UTC (6 years ago) by aloraine

Add Oryza sativa japonica June 2009 and Oryza sativa japonica variety Os-Nipponbare-Reference-IRGSP-1.0 genome assemblies and annotations

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Revision 42 - Directory Listing
Modified Thu Sep 27 15:12:10 2018 UTC (6 years ago) by aloraine

Add Nematostella vectensis, starlet sea anemone

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Revision 41 - Directory Listing
Modified Thu Sep 27 15:11:05 2018 UTC (6 years ago) by aloraine

Add Ovis aries (Feb 2010) sheep (ISGC Ovis_aries_1/oviAri1) genome assembly, collected from UCSC

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Revision 40 - Directory Listing
Modified Thu Sep 27 15:05:33 2018 UTC (6 years ago) by aloraine

Add Medicago truncatula Mt3.0 release from Phytozome v7

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Revision 39 - Directory Listing
Modified Thu Sep 27 14:59:57 2018 UTC (6 years ago) by aloraine

Add mouse genomes mm8, mm9, mm10

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Revision 38 - Directory Listing
Modified Thu Sep 27 14:50:39 2018 UTC (6 years ago) by aloraine

Add Malus domestica Borkh (GDDH13 Version 1.1) apple genome assembly and annotations

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Revision 37 - Directory Listing
Modified Thu Sep 27 14:47:45 2018 UTC (6 years ago) by aloraine

Add Musa acuminata DH Pahang (Jan 2016) banana (v2) genome assembly and annotations

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Revision 36 - Directory Listing
Modified Thu Sep 27 14:41:43 2018 UTC (6 years ago) by aloraine

Add Loxodonta africana (Jul 2009) elephant (loxAfr3), collected from UCSC

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Revision 35 - Directory Listing
Modified Thu Sep 27 14:37:21 2018 UTC (6 years ago) by aloraine

Add Glycine max (soybean) Gmax_275_v2.0 genome assembly and annotations, collected from Phytozome in Feb. 2015

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Revision 34 - Directory Listing
Modified Thu Sep 27 14:34:19 2018 UTC (6 years ago) by aloraine

Add Glycine max Glyma1 soybean genome assembly and annotations, collected from Phytozome

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Revision 33 - Directory Listing
Modified Thu Sep 27 14:30:06 2018 UTC (6 years ago) by aloraine

Add Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0) assembly and annotations, collected from UCSC

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Revision 32 - Directory Listing
Modified Thu Sep 27 14:27:37 2018 UTC (6 years ago) by aloraine

Add Fragaria vesca (woodland strawberry) v1

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Revision 31 - Directory Listing
Modified Thu Sep 27 14:20:07 2018 UTC (6 years ago) by aloraine

Add Felis catus (Sep 2011) cat (ICGSC Felis_catus 6.2/felCat5) genome assembly collected from UCSC

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Revision 30 - Directory Listing
Modified Thu Sep 27 14:17:04 2018 UTC (6 years ago) by aloraine

Add HEADER (same as for UCSC genomes)

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Revision 29 - Directory Listing
Modified Thu Sep 27 14:15:35 2018 UTC (6 years ago) by aloraine

Remove 2008 cat genome; re-order rows

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Revision 28 - Directory Listing
Modified Thu Sep 27 14:13:07 2018 UTC (6 years ago) by aloraine

Add Escherichia coli K12-MG1655 assembly, collected from Genbank record http://www.ncbi.nlm.nih.gov/nuccore/49175990

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Revision 27 - Directory Listing
Modified Thu Sep 27 14:11:41 2018 UTC (6 years ago) by aloraine

Add Equus caballus (Sep 2007) horse (equCab2) genome assembly and annotations

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Revision 26 - Directory Listing
Modified Thu Sep 27 14:08:41 2018 UTC (6 years ago) by aloraine

Add Danio rerio (Jul 2010) zebrafish (danRer7/Zv9) assembly and annotations

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Revision 25 - Directory Listing
Modified Thu Sep 27 14:02:56 2018 UTC (6 years ago) by aloraine

Add Drosophila melanogaster (Jul 2014) fruit fly (dmel_r6.03_FB2014_06) assembly, collected from FlyBase

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Revision 24 - Directory Listing
Modified Thu Sep 27 14:00:32 2018 UTC (6 years ago) by aloraine

Add Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5) assembly, collected from UCSC

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Revision 23 - Directory Listing
Modified Thu Sep 27 13:58:58 2018 UTC (6 years ago) by aloraine

Add Dictyostelim discoideum (slime mold) May 2009 assembly and annotations, from DictyDB

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Revision 22 - Directory Listing
Modified Thu Sep 27 13:57:07 2018 UTC (6 years ago) by aloraine

Add Camelina sativa (false flax) April 2014 assembly

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Revision 21 - Directory Listing
Modified Thu Sep 27 13:55:37 2018 UTC (6 years ago) by aloraine

Add Chlamydomonas reinhardtii JGI v4 assembly

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Revision 20 - Directory Listing
Modified Thu Sep 27 13:54:35 2018 UTC (6 years ago) by aloraine

Add Cavia porcellus (Feb 2008) guinea pig (cavPor3) assembly

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Revision 19 - Directory Listing
Modified Thu Sep 27 13:50:44 2018 UTC (6 years ago) by aloraine

Add Carica papaya genome assembly, from Phytozome

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Revision 18 - Directory Listing
Modified Thu Sep 27 13:48:26 2018 UTC (6 years ago) by aloraine

Add C elegans assembles: May 2008 (WS190/ce6) and Oct 2010 (WS220/ce10)

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Revision 17 - Directory Listing
Modified Thu Sep 27 13:46:05 2018 UTC (6 years ago) by aloraine

Add Homo sapiens Mar 2006 NCBI36/hg18 assembly

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Revision 16 - Directory Listing
Modified Thu Sep 27 13:41:08 2018 UTC (6 years ago) by aloraine

Add Bos taurus (Oct 2011) cow (Baylor Btau_4.6.1/bosTau7)

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Revision 15 - Directory Listing
Modified Thu Sep 27 13:37:28 2018 UTC (6 years ago) by aloraine

Add Homo sapiens Mar 2006 NCBI36/hg18 assembly

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Revision 14 - Directory Listing
Modified Thu Sep 27 13:32:54 2018 UTC (6 years ago) by aloraine

Add Brachypodium distachyon JGI v1.0 8x assembly

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Revision 13 - Directory Listing
Modified Thu Sep 27 13:29:20 2018 UTC (6 years ago) by aloraine

Add TAIR8 genome assembly

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Revision 12 - Directory Listing
Modified Thu Sep 27 13:27:26 2018 UTC (6 years ago) by aloraine

Add latest honeybee assembly Jan 2005 Baylor 2.0/apiMel2

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Revision 11 - Directory Listing
Modified Thu Sep 27 13:19:16 2018 UTC (6 years ago) by aloraine

Add assemblies from www.candidagenome.org

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Revision 10 - Directory Listing
Modified Wed Sep 26 22:23:41 2018 UTC (6 years ago) by aloraine

Add Feb 2009 GRCh37/hg19 human genome assembly

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Revision 9 - Directory Listing
Modified Wed Sep 26 22:18:04 2018 UTC (6 years ago) by aloraine

Add latest human genome version, with annotations, collected by Nowlan Freese

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Revision 8 - Directory Listing
Modified Wed Sep 26 22:01:04 2018 UTC (6 years ago) by aloraine

Describe contents

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Revision 7 - Directory Listing
Modified Wed Sep 26 21:51:10 2018 UTC (6 years ago) by aloraine

Add 2008 budding yeast genome assembly, with annotations; Add contents file with available genomes

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Revision 6 - Directory Listing
Modified Wed Sep 26 21:27:36 2018 UTC (6 years ago) by aloraine

Add latest panda genome assembly

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Revision 5 - Directory Listing
Modified Wed Sep 26 21:15:00 2018 UTC (6 years ago) by aloraine

Add Arabidopsis lyrata genome assembly and annotations, from Phytozome

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Revision 4 - Directory Listing
Modified Wed Sep 26 20:23:53 2018 UTC (6 years ago) by aloraine

Add 2003 mosquito (malaria vector) genome assembly, EST, mRNA, and gene model annotations

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Revision 3 - Directory Listing
Modified Wed Sep 26 20:21:58 2018 UTC (6 years ago) by aloraine

Describe what a Quickload site is

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Revision 2 - Directory Listing
Modified Wed Sep 26 20:18:10 2018 UTC (6 years ago) by aloraine

Show this in place of a folder icon in IGB Available Data Sets browser

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Revision 1 - Directory Listing
Added Wed Sep 26 18:26:11 2018 UTC (6 years ago) by aloraine

Add Arabidopsis thaliana TAIR9/10 genome assembly sequence file and annotations