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<h1>Malus domestica (apple) June 2017 genome assembly</h1>
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<p>
This directory contains annotation and sequence data files from the GDDH13 Version 1.1 apple genome released in June 2017. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB). 
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Files include:
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<ul>
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2bit file - sequence file in two-bit format, created using
faToTwoBit. 
When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>. 
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<li>
annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="https://bioviz.org">Integrated Genome Browser</a>.

<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>

<li>reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
<li>sub-directories with additional data, including mRNA and EST alignments, RNA-Seq data sets, etc. 
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<b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.
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[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[TXT]genome.txt2023-06-16 13:42 270 Chromosome lengths and assembly information
[ ]M_domestica_Borkh_Jun_2017.bed.gz2023-06-16 13:42 2.5MAnnotation or junction file
[ ]M_domestica_Borkh_Jun_2017.bed.gz.tbi2023-06-16 13:42 260KTabix index file
[ ]annots.xml2023-06-16 13:42 359 Annotation and data file list
[ ]M_domestica_Borkh_Jun_2017.2bit2023-06-16 13:42 169MSequence data in blat 2bit format
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