_A_05_MSA_3cvs-GFFmerged

Overview
Related items

Short Name: 05_MSA_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: MSA 3cv and GFF-merged Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

SEEK ID: https://fairdomhub.org/assays/1270

Class: Modelling analysis

Projects: _p_stRT

Investigation: _I_STRT

Study: _S_04_stPanTr

Assay position:

Biological problem addressed: Model Analysis Type

Organisms: No organisms

Help

Tree Split Graph

Export PNG

Click below to download a copy of the image

Download

Creators and Submitter

Creators

Andrej Blejec
Maja Zagorscak

Submitter

Andrej Blejec

Citation

Blejec, A., & Zagorscak, M. (2020). _A_05_MSA_3cvs-GFFmerged. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.ASSAY.1270.2

Note: This is a citation for Snapshot 2 of this Assay, the contents of which may vary from what is shown on this page.

Snapshots

Snapshot 2 (12th Apr 2020) DOI

Snapshot 1 (25th Mar 2020) DOI

Activity

Views: 1326

Created: 19th Mar 2020 at 10:58

Last updated: 12th Apr 2020 at 09:42

Related items

People (2)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Data files (8)
Documents (5)

Advanced People list for this Assay with search and filtering

Andrej Blejec

Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

Institutions: National Institute of Biology, NewHorizon

https://orcid.org/0000-0001-7484-6031

Expertise: Mathematical and statistical modeling, Bioinformatics, Visualization, Statistics, R, Programming, Computational Statistics

Tools: R, Statistical tools, Statistics, Data Management, Computational Systems Biology, Data Integration

Maja Zagorscak

Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2

Institutions: National Institute of Biology, tst

https://orcid.org/0000-0002-1669-6482

Expertise: Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming, Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Visualization, Data Integration, Computational Biology

Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology, Data Integration

Computational Biologist and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)

Advanced Programmes list for this Assay with search and filtering

NIBSys

National Institute of Biology, Department of Biotechnology and Systems Biology projects

Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground

Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology

Advanced Projects list for this Assay with search and filtering

_p_stRT

project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...

Programme: NIBSys

Public web page: http://www.nib.si/eng/index.php/systems-biology

Start date: 1st Dec 2017

End date: 1st Jan 2020

Organisms: Potato virus Y, Solanum tuberosum

Advanced Investigations list for this Assay with search and filtering

_I_STRT

_p_stRT

(Show All)

All creators

Maja Zagorscak

Kristina Gruden

Marko Petek

Ziva Ramsak

Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED ...

Submitter: Maja Zagorscak

Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr

Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged

Snapshots: No snapshots

Created: 24th Oct 2019 at 14:36, Last updated: 26th Nov 2019 at 09:37

Advanced Studies list for this Assay with search and filtering

_S_04_stPanTr

_p_stRT

All creators

Andrej Blejec

Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Investigation: _I_STRT

Assays: _A_01_GC_content-count, _A_02_cdhit_3cvs-GFFmerged, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged

Snapshots: No snapshots

Created: 18th Mar 2020 at 20:44

Advanced Data files list for this Assay with search and filtering

/reports/SupplementaryFile2.html

_p_stRT

All creators

Maja Zagorscak

Supplementary File 2 - Multiple sequence alignments using ClustalOmega v1.2.1 or MAFFT v7.271 and MView v1.66. Paralogue clusters on representative and alternative sequences, at least one from each of the four genotypes. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_05_MSA_3cvs-GFFmerged

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3691.1

Relationship type: Not specified

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_04_stPanTr

Assays: Supplementary Information, _A_05_MSA_3cvs-GFFmerged

Download

Created: 23rd Mar 2020 at 15:54, Last updated: 23rd Mar 2020 at 15:59