<h1>Physcomitrella patens (moss) January 2018 genome assembly</h1>
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<p>
This directory contains annotation and sequence data files from the Physcomitrella patens genome version 3.3 genome released in January 2018. 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.
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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>.
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<li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file.
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<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>.)
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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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To get faToTwoBit and twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
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