{"__v":1,"_id":"574ef700014ddc0e00d14754","category":{"project":"5735936aafab441700723a50","version":"5735936aafab441700723a53","_id":"5735e5f2ec67f6290013ac72","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T14:34:26.031Z","from_sync":false,"order":10,"slug":"configuration-options-compara-import","title":"Configuration Options (Compara Import)"},"parentDoc":null,"project":"5735936aafab441700723a50","user":"573592b84b0ab120000b7d44","version":{"__v":12,"_id":"5735936aafab441700723a53","project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-01T14:53:52.585Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"```\n[METHOD_LINK]\n\tBLASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]\n\tTRANSLATED_BLAT = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]\n\tTRANSLATED_BLAT_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]\n\tPECAN = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.multiple_alignment ]\n\tORTHEUS = [ DNA-DNA_ALIGNMENT GenomicAlignTree.tree_alignment ]\n\tLASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]\n\tATAC = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]\n\tSYNTENY = [ GENOMIC_SYNTENY SyntenyRegion.synteny ]\n\tENSEMBL_ORTHOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]\n\tENSEMBL_PARALOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]\n\tENSEMBL_PROJECTIONS = [ PROTEIN_HOMOLOGY Homology.homology ]\n\tENSEMBL_HOMOEOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]\n\tFAMILY = [ PROTEIN_FAMILY Family.family ]\n\tPROTEIN_TREES = [ PROTEIN-NCRNA_TREE ProteinTree.protein_tree_node ]\n\tGERP_CONSTRAINED_ELEMENT = [ PROTEIN-NCRNA_TREE GenomicAlignBlock.constrained_element ]\n```\nContains names and classes of methods used with the main table in which results are stored.  Each method follows the pattern: ``KEY = [ METHOD_CLASS DATABASE_TABLE.DATA_TYPE ]``.\n\nMethods are defined in this way to ensure consistency with the compara database and the ``METHOD_CLASS`` must be one of:\n- ``DNA-DNA_ALIGNMENT``\n- ``GENOMIC_SYNTENY``\n- ``PROTEIN_HOMOLOGY``\n- ``PROTEIN_FAMILY``\n- ``PROTEIN-NCRNA_TREE``","excerpt":"","slug":"method_link-compara","type":"basic","title":"[METHOD_LINK]"}
``` [METHOD_LINK] BLASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ] TRANSLATED_BLAT = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ] TRANSLATED_BLAT_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ] PECAN = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.multiple_alignment ] ORTHEUS = [ DNA-DNA_ALIGNMENT GenomicAlignTree.tree_alignment ] LASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ] ATAC = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ] SYNTENY = [ GENOMIC_SYNTENY SyntenyRegion.synteny ] ENSEMBL_ORTHOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ] ENSEMBL_PARALOGUES = [ PROTEIN_HOMOLOGY Homology.homology ] ENSEMBL_PROJECTIONS = [ PROTEIN_HOMOLOGY Homology.homology ] ENSEMBL_HOMOEOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ] FAMILY = [ PROTEIN_FAMILY Family.family ] PROTEIN_TREES = [ PROTEIN-NCRNA_TREE ProteinTree.protein_tree_node ] GERP_CONSTRAINED_ELEMENT = [ PROTEIN-NCRNA_TREE GenomicAlignBlock.constrained_element ] ``` Contains names and classes of methods used with the main table in which results are stored. Each method follows the pattern: ``KEY = [ METHOD_CLASS DATABASE_TABLE.DATA_TYPE ]``. Methods are defined in this way to ensure consistency with the compara database and the ``METHOD_CLASS`` must be one of: - ``DNA-DNA_ALIGNMENT`` - ``GENOMIC_SYNTENY`` - ``PROTEIN_HOMOLOGY`` - ``PROTEIN_FAMILY`` - ``PROTEIN-NCRNA_TREE``