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data/community/genspectrum/marburg/HK1980/all-lineages/CHANGELOG.md
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| ## Unreleased | ||
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| First release of Marburg virus dataset. |
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data/community/genspectrum/marburg/HK1980/all-lineages/README.md
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| # Nextclade dataset for "Marburg Virus" based on reference "NC_001608.3" | ||
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| **Orthomarburgvirus marburgense** species taxon (taxonId: 3052505), members of this species are called marburgviruses. However, the species has two distinct lineages: ravn virus (RAVV) and marburg virus (MARV). Alignments use the official INSDC marburg virus reference sequence [NC_001608.3](https://www.ncbi.nlm.nih.gov/nuccore/NC_001608.3). | ||
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| The example sequences are a subsample of 20 Orthomarburgvirus marburgense sequences with over 10% coverage. | ||
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| | Key | Value | | ||
| | ------------ | ------------------------------------------------- | | ||
| | authors | Anna Parker | | ||
| | name | Marburg Virus | | ||
| | reference | NC_001608.3 | | ||
| | dataset path | community/genspectrum/marburg/HK1980/all-lineages | | ||
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| ## Scope of this dataset | ||
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| ## Features | ||
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| This dataset was created using the pipeline in https://github.com/anna-parker/marburg-virus-tree and NCBI Virus. Lineages and clades are assigned using the paper: | ||
| **Gianguglielmo Zehender, Chiara Sorrentino, Carla Veo, Lisa Fiaschi, Sonia Gioffrè, Erika Ebranati, Elisabetta Tanzi, Massimo Ciccozzi, Alessia Lai, Massimo Galli, | ||
| Distribution of Marburg virus in Africa: An evolutionary approach, | ||
| Infection, Genetics and Evolution** | ||
| for clade names; link [here](https://www.sciencedirect.com/science/article/pii/S1567134816302386?via%3Dihub). However, we choose not to show the B.1 clade as with additional samples the grouping is no longer very clear. | ||
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| ## What is Nextclade dataset | ||
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| Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html |
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data/community/genspectrum/marburg/HK1980/all-lineages/examples.fasta
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data/community/genspectrum/marburg/HK1980/all-lineages/genome_annotation.gff3
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| ##gff-version 3 | ||
| #!gff-spec-version 1.21 | ||
| #!processor NCBI annotwriter | ||
| ##sequence-region NC_001608.3 1 19111 | ||
| ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3052505 | ||
| NC_001608.3 RefSeq region 1 19111 . + . ID=NC_001608.3:1..19111;Dbxref=taxon:3052505;country=Kenya;gbkey=Src;genome=genomic;isolate=Marburg virus/H.sapiens-tc/KEN/1980/Mt. Elgon-Musoke;mol_type=viral cRNA;old-name=Lake Victoria marburgvirus | ||
| NC_001608.3 RefSeq sequence_feature 1 48 . + . ID=id-NC_001608.3:1..48;Note=leader region;gbkey=misc_feature | ||
| NC_001608.3 RefSeq gene 49 2844 . + . ID=gene-MARV_gp1;Dbxref=GeneID:920944;Name=NP;gbkey=Gene;gene=NP;gene_biotype=protein_coding;locus_tag=MARV_gp1 | ||
| NC_001608.3 RefSeq mRNA 49 2844 . + . ID=rna-MARV_gp1;Parent=gene-MARV_gp1;Dbxref=GeneID:920944;gbkey=mRNA;gene=NP;locus_tag=MARV_gp1;product=nucleoprotein | ||
| NC_001608.3 RefSeq exon 49 2844 . + . ID=exon-MARV_gp1-1;Parent=rna-MARV_gp1;Dbxref=GeneID:920944;gbkey=mRNA;gene=NP;locus_tag=MARV_gp1;product=nucleoprotein | ||
| NC_001608.3 RefSeq CDS 104 2191 . + 0 Name=NP;ID=cds-YP_001531153.1;Parent=rna-MARV_gp1;Dbxref=GenBank:YP_001531153.1,GeneID:920944;Name=YP_001531153.1;Note=encapsidates RNA genome;gbkey=CDS;gene=NP;locus_tag=MARV_gp1;product=nucleoprotein;protein_id=YP_001531153.1 | ||
| NC_001608.3 RefSeq gene 2854 4410 . + . ID=gene-MARV_gp2;Dbxref=GeneID:920948;Name=VP35;gbkey=Gene;gene=VP35;gene_biotype=protein_coding;locus_tag=MARV_gp2 | ||
| NC_001608.3 RefSeq mRNA 2854 4410 . + . ID=rna-MARV_gp2;Parent=gene-MARV_gp2;Dbxref=GeneID:920948;gbkey=mRNA;gene=VP35;locus_tag=MARV_gp2;product=VP35 | ||
| NC_001608.3 RefSeq exon 2854 4410 . + . ID=exon-MARV_gp2-1;Parent=rna-MARV_gp2;Dbxref=GeneID:920948;gbkey=mRNA;gene=VP35;locus_tag=MARV_gp2;product=VP35 | ||
| NC_001608.3 RefSeq CDS 2945 3934 . + 0 Name=VP35;ID=cds-YP_001531154.1;Parent=rna-MARV_gp2;Dbxref=GenBank:YP_001531154.1,GeneID:920948;Name=YP_001531154.1;Note=polymerase cofactor%3B type I interferon antagonist;gbkey=CDS;gene=VP35;locus_tag=MARV_gp2;product=polymerase complex protein;protein_id=YP_001531154.1 | ||
| NC_001608.3 RefSeq gene 4415 5819 . + . ID=gene-MARV_gp3;Dbxref=GeneID:920947;Name=VP40;gbkey=Gene;gene=VP40;gene_biotype=protein_coding;locus_tag=MARV_gp3 | ||
| NC_001608.3 RefSeq mRNA 4415 5819 . + . ID=rna-MARV_gp3;Parent=gene-MARV_gp3;Dbxref=GeneID:920947;gbkey=mRNA;gene=VP40;locus_tag=MARV_gp3;product=VP40 | ||
| NC_001608.3 RefSeq exon 4415 5819 . + . ID=exon-MARV_gp3-1;Parent=rna-MARV_gp3;Dbxref=GeneID:920947;gbkey=mRNA;gene=VP40;locus_tag=MARV_gp3;product=VP40 | ||
| NC_001608.3 RefSeq CDS 4568 5479 . + 0 Name=VP40;ID=cds-YP_001531155.1;Parent=rna-MARV_gp3;Dbxref=GenBank:YP_001531155.1,GeneID:920947;Name=YP_001531155.1;Note=budding%3B virus particle formation;gbkey=CDS;gene=VP40;locus_tag=MARV_gp3;product=matrix protein;protein_id=YP_001531155.1 | ||
| NC_001608.3 RefSeq gene 5825 8670 . + . ID=gene-MARV_gp4;Dbxref=GeneID:920945;Name=GP;gbkey=Gene;gene=GP;gene_biotype=protein_coding;locus_tag=MARV_gp4 | ||
| NC_001608.3 RefSeq mRNA 5825 8670 . + . ID=rna-MARV_gp4;Parent=gene-MARV_gp4;Dbxref=GeneID:920945;gbkey=mRNA;gene=GP;locus_tag=MARV_gp4;product=glycoprotein | ||
| NC_001608.3 RefSeq exon 5825 8670 . + . ID=exon-MARV_gp4-1;Parent=rna-MARV_gp4;Dbxref=GeneID:920945;gbkey=mRNA;gene=GP;locus_tag=MARV_gp4;product=glycoprotein | ||
| NC_001608.3 RefSeq CDS 5941 7986 . + 0 Name=GP;ID=cds-YP_001531156.1;Parent=rna-MARV_gp4;Dbxref=GenBank:YP_001531156.1,GeneID:920945;Name=YP_001531156.1;Note=fusion%3B receptor binding;gbkey=CDS;gene=GP;locus_tag=MARV_gp4;product=glycoprotein;protein_id=YP_001531156.1 | ||
| NC_001608.3 RefSeq gene 8768 10016 . + . ID=gene-MARV_gp5;Dbxref=GeneID:920942;Name=VP30;gbkey=Gene;gene=VP30;gene_biotype=protein_coding;locus_tag=MARV_gp5 | ||
| NC_001608.3 RefSeq mRNA 8768 10016 . + . ID=rna-MARV_gp5;Parent=gene-MARV_gp5;Dbxref=GeneID:920942;gbkey=mRNA;gene=VP30;locus_tag=MARV_gp5;product=VP30 | ||
| NC_001608.3 RefSeq exon 8768 10016 . + . ID=exon-MARV_gp5-1;Parent=rna-MARV_gp5;Dbxref=GeneID:920942;gbkey=mRNA;gene=VP30;locus_tag=MARV_gp5;product=VP30 | ||
| NC_001608.3 RefSeq CDS 8869 9714 . + 0 Name=VP30;ID=cds-YP_001531157.1;Parent=rna-MARV_gp5;Dbxref=GenBank:YP_001531157.1,GeneID:920942;Name=YP_001531157.1;Note=binds to NP;gbkey=CDS;gene=VP30;locus_tag=MARV_gp5;product=minor nucleoprotein;protein_id=YP_001531157.1 | ||
| NC_001608.3 RefSeq gene 9999 11285 . + . ID=gene-MARV_gp6;Dbxref=GeneID:920943;Name=VP24;gbkey=Gene;gene=VP24;gene_biotype=protein_coding;locus_tag=MARV_gp6 | ||
| NC_001608.3 RefSeq mRNA 9999 11285 . + . ID=rna-MARV_gp6;Parent=gene-MARV_gp6;Dbxref=GeneID:920943;gbkey=mRNA;gene=VP24;locus_tag=MARV_gp6;product=VP24 | ||
| NC_001608.3 RefSeq exon 9999 11285 . + . ID=exon-MARV_gp6-1;Parent=rna-MARV_gp6;Dbxref=GeneID:920943;gbkey=mRNA;gene=VP24;locus_tag=MARV_gp6;product=VP24 | ||
| NC_001608.3 RefSeq CDS 10207 10968 . + 0 Name=VP24;ID=cds-YP_001531158.1;Parent=rna-MARV_gp6;Dbxref=GenBank:YP_001531158.1,GeneID:920943;Name=YP_001531158.1;gbkey=CDS;gene=VP24;locus_tag=MARV_gp6;product=matrix protein;protein_id=YP_001531158.1 | ||
| NC_001608.3 RefSeq gene 11291 19035 . + . ID=gene-MARV_gp7;Dbxref=GeneID:920946;Name=L;gbkey=Gene;gene=L;gene_biotype=protein_coding;locus_tag=MARV_gp7 | ||
| NC_001608.3 RefSeq mRNA 11291 19035 . + . ID=rna-MARV_gp7;Parent=gene-MARV_gp7;Dbxref=GeneID:920946;gbkey=mRNA;gene=L;locus_tag=MARV_gp7;product=L protein | ||
| NC_001608.3 RefSeq exon 11291 19035 . + . ID=exon-MARV_gp7-1;Parent=rna-MARV_gp7;Dbxref=GeneID:920946;gbkey=mRNA;gene=L;locus_tag=MARV_gp7;product=L protein | ||
| NC_001608.3 RefSeq CDS 11481 18476 . + 0 Name=L;ID=cds-YP_001531159.1;Parent=rna-MARV_gp7;Dbxref=GenBank:YP_001531159.1,GeneID:920946;Name=YP_001531159.1;gbkey=CDS;gene=L;locus_tag=MARV_gp7;product=RNA-dependent RNA polymerase;protein_id=YP_001531159.1 | ||
| NC_001608.3 RefSeq sequence_feature 19036 19111 . + . ID=id-NC_001608.3:19036..19111;Note=trailer;gbkey=misc_feature | ||
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