Log of /quickload

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Revision 198 - Directory Listing
Modified Mon Jul 8 20:08:41 2024 UTC (4 months ago) by nfreese

IGBF-3682: Add Ramazzottius varieornatus Nov 2016 genome; Jul 8, 2024

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Revision 197 - Directory Listing
Modified Mon Jul 8 20:08:27 2024 UTC (4 months ago) by nfreese

IGBF-3682: Add Ramazzottius varieornatus Nov 2016 genome; Jul 8, 2024

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Revision 196 - Directory Listing
Modified Mon Jul 8 20:08:11 2024 UTC (4 months ago) by nfreese

IGBF-3682: Add Ramazzottius varieornatus Nov 2016 genome; Jul 8, 2024

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Revision 195 - Directory Listing
Modified Mon Jul 8 20:07:47 2024 UTC (4 months ago) by nfreese

IGBF-3682: Add Ramazzottius varieornatus Nov 2016 genome; Jul 8, 2024

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Revision 194 - Directory Listing
Modified Mon Jul 8 20:07:06 2024 UTC (4 months ago) by nfreese

IGBF-3682: Add Ramazzottius varieornatus Nov 2016 genome; Jul 8, 2024

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Revision 193 - Directory Listing
Modified Fri May 31 16:56:12 2024 UTC (5 months, 1 week ago) by nfreese

IGBF-3666: Remove return carriages in D melanogaster Aug 2014 refGene annotation;May 31, 2024

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Revision 192 - Directory Listing
Modified Fri May 31 16:55:44 2024 UTC (5 months, 1 week ago) by nfreese

IGBF-3666: Remove return carriages in D melanogaster Aug 2014 refGene annotation;May 31, 2024

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Revision 191 - Directory Listing
Modified Tue May 28 17:52:16 2024 UTC (5 months, 1 week ago) by aloraine

IGBF-3172 Include F3H and enzyme name in description for Solyc02g083860 in SL4

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Revision 190 - Directory Listing
Modified Tue May 28 17:51:15 2024 UTC (5 months, 1 week ago) by aloraine

IGBF-3172 Include F3H and enzyme name in description for PRAM_26184 in SL5

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Revision 189 - Directory Listing
Modified Tue May 28 16:31:28 2024 UTC (5 months, 1 week ago) by aloraine

IGBF-3712 Improve gene description for anthocyanin-reduced (are) in SL5

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Revision 188 - Directory Listing
Modified Wed May 22 12:19:16 2024 UTC (5 months, 2 weeks ago) by aloraine

IGBF-3172 Include F3H and enzyme name in description for solyc02g083860 in SL4

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Revision 187 - Directory Listing
Modified Wed May 22 12:18:18 2024 UTC (5 months, 2 weeks ago) by aloraine

IGBF-3172 Include F3H and enzyme name in description for PRAM_26184 in SL5

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Revision 186 - Directory Listing
Modified Wed Apr 24 16:10:04 2024 UTC (6 months, 2 weeks ago) by pkulzer

IGBF-3682: Fix typo in annots.xml; Apr 24, 2024

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Revision 185 - Directory Listing
Modified Thu Apr 11 21:21:44 2024 UTC (6 months, 4 weeks ago) by aloraine

Include fasta file for user's convenience

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Revision 184 - Directory Listing
Modified Thu Apr 11 04:57:16 2024 UTC (6 months, 4 weeks ago) by aloraine

Create gtf file from bed annotation file suitable for nf-core rnaseq pipeline

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Revision 183 - Directory Listing
Modified Thu Apr 4 13:49:07 2024 UTC (7 months ago) by pkulzer

IGBF-1122: Update S. pombe URL attribute; Apr 4, 2024

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Revision 182 - Directory Listing
Modified Wed Apr 3 20:15:11 2024 UTC (7 months, 1 week ago) by aloraine

IGBF-3682 Strain not straing

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Revision 181 - Directory Listing
Modified Wed Apr 3 19:37:19 2024 UTC (7 months, 1 week ago) by aloraine

Support tardigrade (water bear) Hypsibius exemplaris strain Z151 nHd_3.1 genome assembly  

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Revision 180 - Directory Listing
Modified Fri Sep 15 15:43:45 2023 UTC (13 months, 3 weeks ago) by aloraine

IGBF-3395 Improve formatting

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Revision 179 - Directory Listing
Modified Fri Sep 15 15:41:40 2023 UTC (13 months, 3 weeks ago) by aloraine

IGBF-3395 Fix svn command error; fix typo following review by NF

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Revision 178 - Directory Listing
Modified Tue Aug 15 13:23:11 2023 UTC (14 months, 3 weeks ago) by aloraine

IGBF-3395 Improve documentation

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Revision 177 - Directory Listing
Modified Mon Aug 14 14:16:52 2023 UTC (14 months, 3 weeks ago) by aloraine

IGBF-3395 IGBF-3173 Get code from lorainelab CDN address

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Revision 176 - Directory Listing
Modified Thu Jun 29 18:23:49 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023

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Revision 175 - Directory Listing
Modified Thu Jun 29 18:22:14 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023

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Revision 174 - Directory Listing
Modified Thu Jun 29 18:22:07 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3362: Add Rattus norvegicus Nov 2020 genome;Jun 29, 2023

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Revision 173 - Directory Listing
Modified Thu Jun 29 17:46:56 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023

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Revision 172 - Directory Listing
Modified Thu Jun 29 17:42:46 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023

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Revision 171 - Directory Listing
Modified Thu Jun 29 17:42:26 2023 UTC (16 months, 1 week ago) by nfreese

IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023

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Revision 170 - Directory Listing
Modified Mon Mar 6 03:09:32 2023 UTC (20 months ago) by aloraine

IGBF-3256 Show CHESS version 3.0 gene models for hg38

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Revision 169 - Directory Listing
Modified Fri Feb 10 18:01:40 2023 UTC (20 months, 4 weeks ago) by aloraine

IGBF-3145 Include SL4 locus name in transferred-to-SL5 description

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Revision 168 - Directory Listing
Modified Thu Dec 22 20:28:18 2022 UTC (22 months, 2 weeks ago) by aloraine

IGBF-3229 Transfer SL4 annotations to SL5 models

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Revision 167 - Directory Listing
Modified Wed Sep 21 19:05:34 2022 UTC (2 years, 1 month ago) by aloraine

IGBF-3173 Use github link to obtain js code for strapdown indexing

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Revision 166 - Directory Listing
Modified Wed Jul 6 11:47:14 2022 UTC (2 years, 4 months ago) by aloraine

IGBF-3135 Add SL5.0 tomato genome

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Revision 165 - Directory Listing
Modified Wed Jul 6 11:36:45 2022 UTC (2 years, 4 months ago) by aloraine

IGBF-3135 Add SL5.0 tomato genome

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Revision 164 - Directory Listing
Modified Wed Jul 6 11:36:16 2022 UTC (2 years, 4 months ago) by aloraine

IGBF-3135 Add SL5.0 tomato genome

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Revision 163 - Directory Listing
Modified Mon Nov 22 22:49:46 2021 UTC (2 years, 11 months ago) by nfreese

IGBF-2952: Add Drosophila melanogaster Aug 2014 genome;Nov 22, 2021

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Revision 162 - Directory Listing
Modified Mon Nov 22 22:45:36 2021 UTC (2 years, 11 months ago) by nfreese

IGBF-2952: Add Drosophila melanogaster Aug 2014 genome;Nov 22, 2021

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Revision 161 - Directory Listing
Modified Mon Nov 22 22:45:28 2021 UTC (2 years, 11 months ago) by nfreese

IGBF-2952: Add Drosophila melanogaster Aug 2014 genome;Nov 22, 2021

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Revision 160 - Directory Listing
Modified Wed Sep 22 20:49:05 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add mm10 ENCODE blacklist v2;Sep 22, 2021

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Revision 159 - Directory Listing
Modified Wed Sep 22 20:47:24 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add hg19 ENCODE blacklist v2;Sep 22, 2021

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Revision 158 - Directory Listing
Modified Wed Sep 22 20:46:16 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add hg38 ENCODE blacklist v2;Sep 22, 2021

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Revision 157 - Directory Listing
Modified Wed Sep 22 20:44:46 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add dm3 ENCODE blacklist v2;Sep 22, 2021

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Revision 156 - Directory Listing
Modified Wed Sep 22 20:43:12 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add ce10 ENCODE blacklist v2;Sep 22, 2021

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Revision 155 - Directory Listing
Modified Wed Sep 22 20:41:18 2021 UTC (3 years, 1 month ago) by nfreese

IGBF-2696;Add ce11 ENCODE blacklist v2;Sep 22, 2021

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Revision 154 - Directory Listing
Modified Mon Mar 29 13:35:43 2021 UTC (3 years, 7 months ago) by nfreese

IGBF-2803:Add Ficedula albicollis genome;Mar 29, 2021

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Revision 153 - Directory Listing
Modified Mon Mar 29 13:33:21 2021 UTC (3 years, 7 months ago) by nfreese

IGBF-2803:Add Ficedula albicollis genome;Mar 29, 2021

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Revision 152 - Directory Listing
Modified Mon Mar 29 13:33:06 2021 UTC (3 years, 7 months ago) by nfreese

IGBF-2803:Add Ficedula albicollis genome;Mar 29, 2021

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Revision 151 - Directory Listing
Modified Tue Mar 9 20:00:38 2021 UTC (3 years, 8 months ago) by aloraine

Specify disk space required to replicate the data

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Revision 150 - Directory Listing
Modified Tue Mar 9 19:55:59 2021 UTC (3 years, 8 months ago) by aloraine

Explain how to replicate main Quickload

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Revision 149 - Directory Listing
Modified Wed Mar 3 15:02:07 2021 UTC (3 years, 8 months ago) by aloraine

Add Physcomitrella Jan 2018 v3.3 genome and annotations from Phytozome 318

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Revision 148 - Directory Listing
Modified Tue Feb 2 14:50:24 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in protein match;Feb 2, 2021

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Revision 147 - Directory Listing
Modified Tue Feb 2 14:48:38 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in mRNA;Feb 2, 2021

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Revision 146 - Directory Listing
Modified Tue Feb 2 14:48:00 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in match;Feb 2, 2021

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Revision 145 - Directory Listing
Modified Tue Feb 2 14:46:34 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in gene;Feb 2, 2021

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Revision 144 - Directory Listing
Modified Tue Feb 2 14:45:49 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in expressed sequence match;Feb 2, 2021

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Revision 143 - Directory Listing
Modified Tue Feb 2 14:44:12 2021 UTC (3 years, 9 months ago) by nfreese

Fixx off by one in Exon;Feb 2, 2021

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Revision 142 - Directory Listing
Modified Tue Feb 2 14:43:04 2021 UTC (3 years, 9 months ago) by nfreese

Fix off by one in CDS;Feb 2, 2021

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Revision 141 - Directory Listing
Modified Fri Jan 1 18:13:00 2021 UTC (3 years, 10 months ago) by aloraine

Add Physcomitrella Jan 2018 v3.3 genome and annotations from Phytozome 318

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Revision 140 - Directory Listing
Modified Fri Jan 1 18:12:10 2021 UTC (3 years, 10 months ago) by aloraine

Add Physcomitrella Jan 2018 v3.3 genome and annotations from Phytozome 318

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Revision 139 - Directory Listing
Modified Tue Nov 10 22:13:28 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim match file;Nov 10, 2020

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Revision 138 - Directory Listing
Modified Tue Nov 10 22:12:57 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim mRNA file;Nov 10, 2020

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Revision 137 - Directory Listing
Modified Tue Nov 10 22:11:02 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim gene file;Nov 10, 2020

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Revision 136 - Directory Listing
Modified Tue Nov 10 22:10:22 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim protein match file;Nov 10, 2020

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Revision 135 - Directory Listing
Modified Tue Nov 10 22:09:42 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim expressed sequence match file;Nov 10, 2020

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Revision 134 - Directory Listing
Modified Tue Nov 10 22:06:52 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim Exon file;Nov 10, 2020

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Revision 133 - Directory Listing
Modified Tue Nov 10 22:05:49 2020 UTC (4 years ago) by nfreese

Fix Lotmaria passim CDS file;Nov 10, 2020

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Revision 132 - Directory Listing
Modified Fri Oct 2 17:27:00 2020 UTC (4 years, 1 month ago) by nfreese

Update dbSNP common SNPs to 153

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Revision 131 - Directory Listing
Modified Fri Oct 2 17:22:03 2020 UTC (4 years, 1 month ago) by nfreese

Update descriptions, change to snp153

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Revision 130 - Directory Listing
Modified Fri Oct 2 17:00:48 2020 UTC (4 years, 1 month ago) by nfreese

Update human RefGene;Sep 30, 2020

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Revision 129 - Directory Listing
Modified Fri Oct 2 16:57:37 2020 UTC (4 years, 1 month ago) by nfreese

Update human NCBI RefSeq Curated;Sep 23, 2020

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Revision 128 - Directory Listing
Modified Fri Oct 2 16:54:49 2020 UTC (4 years, 1 month ago) by nfreese

Update human NCBI RefSeq All;Sep 23, 2020

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Revision 127 - Directory Listing
Modified Fri Oct 2 16:46:40 2020 UTC (4 years, 1 month ago) by nfreese

Update human mRNA alignments;Sep 30, 2020

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Revision 126 - Directory Listing
Modified Fri Oct 2 16:42:48 2020 UTC (4 years, 1 month ago) by nfreese

Update human EST alignments;Sep 30, 2020

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Revision 125 - Directory Listing
Modified Mon Sep 28 20:36:47 2020 UTC (4 years, 1 month ago) by aloraine

IGBF-2548 Use uncompressed file to distribute gene models

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Revision 124 - Directory Listing
Modified Thu Sep 24 04:24:57 2020 UTC (4 years, 1 month ago) by aloraine

IGBF-2333 Add wheat genome

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Revision 123 - Directory Listing
Modified Thu Sep 24 03:43:09 2020 UTC (4 years, 1 month ago) by aloraine

IGBF-2333 Add wheat genome

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Revision 122 - Directory Listing
Modified Wed May 27 02:16:15 2020 UTC (4 years, 5 months ago) by aloraine

IGBF-2400 Add C_sativa_CBDRx_Dec_2018 genome

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Revision 121 - Directory Listing
Modified Sun Mar 1 20:45:20 2020 UTC (4 years, 8 months ago) by aloraine

List un-assembled contig last

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Revision 120 - Directory Listing
Modified Sun Mar 1 17:02:33 2020 UTC (4 years, 8 months ago) by aloraine

Add multi-exon Cufflinks gene models from article titled Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato https://www.ncbi.nlm.nih.gov/pubmed/31191588

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Revision 119 - Directory Listing
Modified Tue Feb 18 21:10:52 2020 UTC (4 years, 8 months ago) by aloraine

Add sequence and annotations for tomato SL4.0 genome from ftp.solgenomics.net

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Revision 118 - Directory Listing
Modified Tue Feb 18 21:07:58 2020 UTC (4 years, 8 months ago) by aloraine

Add sequence and annotations for tomato SL4.0 genome from ftp.solgenomics.net

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Revision 117 - Directory Listing
Modified Sun Feb 16 05:33:25 2020 UTC (4 years, 8 months ago) by aloraine

Update budding yeast gene model annotations and annots.xml configuration

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Revision 116 - Directory Listing
Modified Sun Feb 16 04:35:23 2020 UTC (4 years, 8 months ago) by aloraine

Add Xenopus tropicalis Jul 2016 assembly with RefSeq All (ncbiRefSeq) gene model annotations

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Revision 115 - Directory Listing
Modified Sun Feb 16 03:49:40 2020 UTC (4 years, 8 months ago) by aloraine

Add Xenopus tropicalis Jul 2016 assembly with RefSeq All (ncbiRefSeq) gene model annotations

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Revision 114 - Directory Listing
Modified Thu Feb 6 22:35:45 2020 UTC (4 years, 9 months ago) by aloraine

Update ce11 C elegans Feb 2013 assembly with data downloaded Feb. 6, 2020

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Revision 113 - Directory Listing
Modified Wed Sep 11 17:48:24 2019 UTC (5 years, 2 months ago) by aloraine

Use correct URL; Fix typo

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Revision 112 - Directory Listing
Modified Tue Sep 10 21:25:26 2019 UTC (5 years, 2 months ago) by aloraine

Include grcH38P12 (patch12) as synonym for H_sapiens_Dec_2013

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Revision 111 - Directory Listing
Modified Tue Sep 10 21:19:18 2019 UTC (5 years, 2 months ago) by aloraine

IGBF-1492 - Add note indicating FlyBase models came from FlyBase original GFF

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Revision 110 - Directory Listing
Modified Tue Sep 10 21:17:00 2019 UTC (5 years, 2 months ago) by aloraine

Load FlyBase models by default for now, but offer new ones too

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Revision 109 - Directory Listing
Modified Tue Sep 10 21:10:23 2019 UTC (5 years, 2 months ago) by aloraine

Use gene models from UCSC ensGene table, still offer old FlyBase models

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Revision 108 - Directory Listing
Modified Tue Sep 10 20:35:41 2019 UTC (5 years, 2 months ago) by aloraine

IGBF-1915 - Add water flea (Daphnia) genomes

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Revision 107 - Directory Listing
Modified Tue Sep 10 20:30:03 2019 UTC (5 years, 2 months 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, 2 months 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, 2 months 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, 2 months 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, 2 months 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 9 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, 9 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, 9 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, 10 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, 11 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, 11 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 (6 years 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 (6 years ago) by aloraine

Add rat genome rn6

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Revision 82 - Directory Listing
Modified Mon Nov 5 23:25:44 2018 UTC (6 years ago) by aloraine

Add rn6 (rat)

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Revision 81 - Directory Listing
Modified Sat Oct 27 01:49:24 2018 UTC (6 years 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 (6 years 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 (6 years 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 (6 years 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 (6 years 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month ago) by aloraine

Describe contents

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Revision 7 - Directory Listing
Modified Wed Sep 26 21:51:10 2018 UTC (6 years, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month 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, 1 month ago) by aloraine

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