Diamond database for taxonomic annotation of fungal metatranscriptomics
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This is a protein fasta dataset for use with diamond. The <strong>fasta.gz</strong> file contains protein sequences for the following: 1,164 genomes downloaded from JGI (<strong>taxonomy_taxids.tsv</strong>) 121 genomes that are part of the taxmapper database (<strong>taxmapper_taxonomy_taxids.tsv</strong>) of which 6 were fungal the <em>Hygrophorus russula </em>MG78<em> </em>genome downloaded from NCBI. For the <em>H. russula</em> genome, genes were predicted using Augustus (v. 3.2.3) with the laccaria_bicolor model. The final protein database consists of a total of 17,694,143 protein sequences (14,976,193 from JGI, 2,708,401 from taxmapper and 9,549 from <em>H. russula</em>). The fasta file and associated taxonomic information files (nodes.dmp.gz & taxonmap.gz) can be used to build a diamond database compatible with diamond version 0.9.22: <pre><code class="language-bash">zcat fasta.gz | diamond makedb -d diamond --taxonmap taxonmap.gz --taxonnodes nodes.dmp</code></pre>
本数据集为适配DIAMOND软件的蛋白质FASTA数据集。其中的fasta.gz压缩文件包含以下来源的蛋白质序列：从JGI下载的1164个基因组（对应taxonomy_taxids.tsv文件）、隶属于taxmapper数据库的121个基因组（对应taxmapper_taxonomy_taxids.tsv文件，其中6个为真菌物种），以及从NCBI下载的红蜡伞（Hygrophorus russula）MG78基因组。针对该红蜡伞基因组，研究人员使用Augustus（v3.2.3）软件并采用双孢紫皮菇（Laccaria bicolor）的预测模型完成了基因预测。最终的蛋白质数据库总计包含17,694,143条蛋白质序列：其中14,976,193条来自JGI来源，2,708,401条来自taxmapper数据库，9,549条来自红蜡伞基因组。该FASTA文件及关联的分类学信息文件（nodes.dmp.gz与taxonmap.gz）可用于构建适配DIAMOND 0.9.22版本的数据库，具体构建命令如下： bash zcat fasta.gz | diamond makedb -d diamond --taxonmap taxonmap.gz --taxonnodes nodes.dmp
