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ShareScore release 0.9.0
Dataset results
8 results for “SV annotation”
Supplementary material 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The sequences renamed during the workshop. The INSDC accession number, the original INSDC name, and the new UNITE name are shown :
Supplementary material 3 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The metadata annotations for the sequences that were found in the same SHs as sequences from the built environment :
GREEN-VARAN SV annotation resources
<p>This dataset contains a collection of BED files prepared to be used with the SV_annotation tool, part of GREEN-VARAN.</p> <p><strong>GREEN-DB regions</strong></p> <p>Regulatory regions collected in GREEN-DB (see <a href="https://github.com/edg1983/GREEN-VARAN">https://github.com/edg1983/GREEN-VARAN</a>)</p> <p><strong>Population AF annotations</strong></p> <p>These files represent SVs from gnomAD v.2.1.1, 1000G phase3, and the IMH dataset. When not directly available, the GRCh38 versions are obtained by coordinates liftover from GRCh37.</p> <p>If you use AF annotations don't forget to cite also the original papers:</p> <ul> <li>gnomAD paper as described in <a href="https://gnomad.broadinstitute.org/terms">https://gnomad.broadinstitute.org/terms</a></li> <li>1000G SV paper: <a href="https://www.nature.com/articles/nature15394">https://www.nature.com/articles/nature15394</a></li> <li>the original IMH publication <a href="https://www.nature.com/articles/s41586-020-2371-0">https://www.nature.com/articles/s41586-020-2371-0</a></li> </ul> <p><strong>Gene annotations</strong></p> <p>Genes and CDSs annotations are from GENCODE v33 basic set</p>
Supplementary material 4 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The interactive Krona chart associated with Figure 2 :
Supplementary material 2 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The MIxS-BE annotations implemented for the built environment sequences during the workshop :
Figure 3 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 3 Analysis of the MIxS-BE "building occupancy type" (type of building where the underlying sample was taken). The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
Figure 2 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 2 Krona chart of the taxonomic affiliation of the built environment sequences down to order level. The Krona chart lists all annotated built environment sequences except those classified as Fungi sp. (32%) and those of non-fungal origin (1%). An interactive version of the Krona chart is provided as Supplementary material 4. The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
Figure 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 1 Analysis of the built environment sequences for country of collection. Country centroids based on the geographical centres of contiguous country land masses are marked with bubbles of different size on the global map to indicate the number of built environment sequences originating from these countries as stated explicitly in the underlying INSDC records or as restored during the present effort and in Abarenkov et al. (2016) (57 distinct countries, sequence count ranging from 1 to 3,091). The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
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