cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17716736
title: Elution profiles and protein interaction data accompanying "Ancient eukaryotic protein interactions illuminate modern genetic disorders"

description:  






DESCRIPTION



FILENAME



LOCATION





LECA 10K OG set



TableS1-LECA_OGs_annotated.csv



Paper, Table S1

Zenodo





Summary of biological resources



resource_summary.xlsx



STAR Methods





LECA interactome (complexes)



leca_ppis_fdr10_clustered_annotated.xlsx



Paper, Table S2

Zenodo





CFMS - ref proteomes



cfms_ref_proteomes.xlsx



Paper, Table S3

Zenodo





ML - top algorithms



tpot_top_algorithms.xlsx



Paper, Table S4

Zenodo





LECA interactome (pairwise)



leca_ppis_fdr10_pairwise.csv



Zenodo





UniProt Subcellular Localization IDs



uniprot_localization_codes.xlsx



Zenodo





Dollo parsimony - ref proteomes



dollo_parsimony_ref_proteomes.xlsx



Zenodo





Dollo parsimony - input trait matrix



dollo_parsimony_count_matrix.tsv



Zenodo





CFMS - raw elution profiles



amorphea_raw_elution_vectors.csv

excavata_raw_elution_vectors.csv

tsar_raw_elution_vectors.csv

archaeplastida_raw_elution_vectors.csv



Zenodo





CFMS - normalized elution profiles



amorphea_norm_elution_vectors.csv

excavata_norm_elution_vectors.csv

tsar_norm_elution_vectors.csv

archaeplastida_norm_elution_vectors.csv



Zenodo





CFMS/APMS - complete feature matrix



feature_matrix.csv



Zenodo





ML - top features



linearsvc_top_100_features.xlsx



Zenodo





OMIM disease propagation, statistics



omim_disease_propagation_stats.xlsx



Zenodo





OMIM disease propagation, top 20 hits per disease



omim_disease_propagation_top20hits_per_disease.xlsx



Zenodo





Curated OMIM gene-disease relationships for LECA OGs



omim_disease_network.tsv



Zenodo



Curated OMIM gene-disease relationships for human UniProt IDs
omim_disease_groups.csv
Zenodo


Summary of mass spectrometry results for each orthogroup by eukaryotic supergroup
SummaryofMSSupportbySupergroup.xlsx
Zenodo


Summary of phenotype predictions in yeast and Chlamydomonas
LECA_yeast_Chlamy_gene-phenotype-predictions.xlsx
Zenodo


Chlamydomonas mutant phenotype gene sets
Chlamy_mutant_phenotype_gene_sets.tsv
Zenodo


Yeast mutant phenotype gene sets
Yeast_mutant_phenotype_gene_sets.tsv
Zenodo


Binarized species tree for Notung analysis
speciestree_binary_internalnodes.nhx
Zenodo


Notung calls for "famPresent" at 70% confidence
DTL70_famPresent.txt
Zenodo


Notung calls for "origin" at 70% confidence
DTL70_origin.txt
Zenodo


Notung DTL-reconciled trees at 70% confidence
DTL70_trees.zip
Zenodo


Notung calls for "famPresent" at 90% confidence
DTL90_famPresent.txt
Zenodo


Notung calls for "origin" at 90% confidence
DTL90_origin.txt
Zenodo


Notung DTL-reconciled trees at 90% confidence
DTL90_trees.zip
Zenodo
DOI: 10.5281/zenodo.10961422
title: Elution profiles and protein interaction data accompanying "Ancient eukaryotic protein interactions illuminate modern genetic disorders"

description:  






DESCRIPTION



FILENAME



LOCATION





LECA 10K OG set



TableS1-LECA_OGs_annotated.csv



Paper, Table S1

Zenodo





Summary of biological resources



resource_summary.xlsx



STAR Methods





LECA interactome (complexes)



leca_ppis_fdr10_clustered_annotated.xlsx



Paper, Table S2

Zenodo





CFMS - ref proteomes



cfms_ref_proteomes.xlsx



Paper, Table S3

Zenodo





ML - top algorithms



tpot_top_algorithms.xlsx



Paper, Table S4

Zenodo





LECA interactome (pairwise)



leca_ppis_fdr10_pairwise.csv



Zenodo





UniProt Subcellular Localization IDs



uniprot_localization_codes.xlsx



Zenodo





Dollo parsimony - ref proteomes



dollo_parsimony_ref_proteomes.xlsx



Zenodo





Dollo parsimony - input trait matrix



dollo_parsimony_count_matrix.tsv



Zenodo





CFMS - raw elution profiles



amorphea_raw_elution_vectors.csv

excavata_raw_elution_vectors.csv

tsar_raw_elution_vectors.csv

archaeplastida_raw_elution_vectors.csv



Zenodo





CFMS - normalized elution profiles



amorphea_norm_elution_vectors.csv

excavata_norm_elution_vectors.csv

tsar_norm_elution_vectors.csv

archaeplastida_norm_elution_vectors.csv



Zenodo





CFMS/APMS - complete feature matrix



feature_matrix.csv



Zenodo





ML - top features



linearsvc_top_100_features.xlsx



Zenodo





OMIM disease propagation, statistics



omim_disease_propagation_stats.xlsx



Zenodo





OMIM disease propagation, top 20 hits per disease



omim_disease_propagation_top20hits_per_disease.xlsx



Zenodo





Curated OMIM gene-disease relationships for LECA OGs



omim_disease_network.tsv



Zenodo



Curated OMIM gene-disease relationships for human UniProt IDs
omim_disease_groups.csv
Zenodo


Summary of mass spectrometry results for each orthogroup by eukaryotic supergroup
SummaryofMSSupportbySupergroup.xlsx
Zenodo


Summary of phenotype predictions in yeast and Chlamydomonas
LECA_yeast_Chlamy_gene-phenotype-predictions.xlsx
Zenodo


Chlamydomonas mutant phenotype gene sets
Chlamy_mutant_phenotype_gene_sets.tsv
Zenodo


Yeast mutant phenotype gene sets
Yeast_mutant_phenotype_gene_sets.tsv
Zenodo


Binarized species tree for Notung analysis
speciestree_binary_internalnodes.nhx
Zenodo


Notung calls for "famPresent" at 70% confidence
DTL70_famPresent.txt
Zenodo


Notung calls for "origin" at 70% confidence
DTL70_origin.txt
Zenodo


Notung DTL-reconciled trees at 70% confidence
DTL70_trees.zip
Zenodo


Notung calls for "famPresent" at 90% confidence
DTL90_famPresent.txt
Zenodo


Notung calls for "origin" at 90% confidence
DTL90_origin.txt
Zenodo


Notung DTL-reconciled trees at 90% confidence
DTL90_trees.zip
Zenodo
DOI: 10.5064/f6g2petf/dv09hg
title: Moore-et-al_CT_0821_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/hipqbi
title: Moore-et-al_CT_0521_Governor Lamont Announces Launch of _Say Yes to Connecticut_ Summer Tourism Campaign.pdf
DOI: 10.5064/f6g2petf/smaf5a
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_06.pdf
DOI: 10.5064/f6g2petf/bhrnso
title: Moore-et-al_CT_0421_Attorney General Tong Urges OfferUp to Stop Sales of Fake Vaccination Cards.pdf
DOI: 10.5064/f6g2petf/mkh5jy
title: Moore-et-al_CT_0621_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/jmdqlp
title: Moore-et-al_CT_0121_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/gypftw
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/kmwtet
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut's Coronavirus Response Efforts.pdf
DOI: 10.5064/f6g2petf/wikw67
title: Moore-et-al_CT_0521_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/jovvma
title: Moore-et-al_CT_0321_Governor Lamont Provides Update on Connecticut's Coronavirus Response Efforts_01.pdf
DOI: 10.5064/f6g2petf/pi8jrs
title: Moore-et-al_CT_1220_Governor Lamont Announces Connecticut Vaccine Distribution Plan To Begin.pdf
DOI: 10.5064/f6g2petf/lpar7g
title: Moore-et-al_CT_0121_Governor Lamont's 2021 State of the State Address.pdf
DOI: 10.5064/f6g2petf/fqhd9q
title: Moore-et-al_CT_0721_Are there walk-up vaccine clinics in Connecticut_.pdf
DOI: 10.5064/f6g2petf/xdqjq5
title: Moore-et-al_CT_0921_What vaccine and testing information do I need to submit to the state as a contractor_ Do I need to retain anyth.pdf
DOI: 10.5064/f6g2petf/jvg8wm
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_10.pdf
DOI: 10.5064/f6g2petf/fdluk4
title: Moore-et-al_CT_0521_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts.pdf
DOI: 10.5064/f6g2petf/ow96po
title: Moore-et-al_CT_0321_Governor Lamont Announces Accelerated Schedule To Provide COVID-19 Vaccines To Connecticut Residents as Quickly .pdf
DOI: 10.5064/f6g2petf/uz4rpr
title: Moore-et-al_CT_0121_Governor Lamont Appointed Co-Chair of National Governors Association’s Pandemic and Disaster Response Task Force.pdf
DOI: 10.5064/f6g2petf/3tfppy
title: Moore-et-al_CT_0821_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/z9mig2
title: Moore-et-al_CT_0721_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/cxuele
title: Moore-et-al_CT_0321_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/bktb4o
title: Moore-et-al_CT_0621_Rock The Shot FAQs.pdf
DOI: 10.5064/f6g2petf/mhvbcn
title: Moore-et-al_CT_0821_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_06.pdf
DOI: 10.5064/f6g2petf/xeyxff
title: Moore-et-al_CT_0521_Will the DPH Van Clinics be Coming to My Area_.pdf
DOI: 10.5064/f6g2petf/fyrbhs
title: Moore-et-al_CT_0721_Is it safe to get vaccinated if I have an underlying health condition_.pdf
DOI: 10.5064/f6g2petf/oihvso
title: Moore-et-al_CT_0821_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/ys26qz
title: Moore-et-al_CT_0621_DDS_COVID-19_Post-Vaccine_Exposure_Guidance-revised_FINAL_6-21-2021.pdf
DOI: 10.5064/f6g2petf/8pkqdw
title: Moore-et-al_CT_0621_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/rrg3f0
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/r1pm2c
title: Moore-et-al_CT_0921_Do long term care facility employees have to be vaccinated against COVID-19_.pdf
DOI: 10.5064/f6g2petf/kaqdfr
title: Moore-et-al_CT_0921_Connecticut Department Of Public Health Issues Statement.pdf
DOI: 10.5064/f6g2petf/186rxl
title: Moore-et-al_CT_0121_COVID-19-Vaccine-Providers-Manual-01312021.pdf
DOI: 10.5064/f6g2petf/1bryyi
title: Moore-et-al_CT_0721_20210713-declaration-of-civil-preparedness-and-public-health-emergencies.pdf
DOI: 10.5064/f6g2petf/wxhuih
title: Moore-et-al_CT_0621_Governor Lamont Launches ‘Rock the Shot’ Campaign Giving Those Who Are Vaccinated a Chance To Win Concert Ticket.pdf
DOI: 10.5064/f6g2petf/wueoza
title: Moore-et-al_CT_0421_State Department of Education and Department of Public Health release Finish Strong guidance.pdf
DOI: 10.5064/f6g2petf/wntsqq
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_06.pdf
DOI: 10.5281/zenodo.17704803
title: Diatoms in the headwaters of the Volga River (raw data from the Upper Volga Expedition 2005)

description: In August 2005, in the headwaters of the Volga River upstream of Tver, 27 diatom samples (18 from the Volga and 9 from selected tributaries) were collected. This dataset, from the Upper Volga Expedition 2005, provides a first comprehensive checklist of benthic diatoms for the Volga headwaters. We provide metadata (sampling date, coordinates) and original counts as well as relative abundances.
DOI: 10.5281/zenodo.17704802
title: Diatoms in the headwaters of the Volga River (raw data from the Upper Volga Expedition 2005)

description: In August 2005, in the headwaters of the Volga River upstream of Tver, 27 diatom samples (18 from the Volga and 9 from selected tributaries) were collected. This dataset, from the Upper Volga Expedition 2005, provides a first comprehensive checklist of benthic diatoms for the Volga headwaters. We provide metadata (sampling date, coordinates) and original counts as well as relative abundances.
DOI: 10.5064/f6g2petf/ihw8zm
title: Moore-et-al_CT_0521_Executive-Order-No-12A.pdf
DOI: 10.5064/f6g2petf/hmwnmv
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/vycgfv
title: Moore-et-al_CT_0121_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_04.pdf
DOI: 10.5064/f6g2petf/4b8lhk
title: Moore-et-al_CT_0121_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/342bg3
title: Moore-et-al_CT_0521_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/3hj4qy
title: Moore-et-al_CT_0221_Governor Lamont Announces Connecticut Will Continue Age-Based Approach To COVID-19 Vaccine Eligibility_ Educator.pdf
DOI: 10.5064/f6g2petf/ziocce
title: Moore-et-al_CT_0321_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/slj7c0
title: Moore-et-al_CT_0921_Connecticut Department of Public Health Issues Statement Regarding ACIP Guidance On Boosters.pdf
DOI: 10.5064/f6g2petf/lygt84
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_04.pdf
DOI: 10.5064/f6g2petf/wzlx9h
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/ijdoxz
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/4bxpya
title: Moore-et-al_CT_0921_Connecticut DPH Issues Statement Regarding FDA Vaccine Advisors Vote.pdf
DOI: 10.5064/f6g2petf/jnozho
title: Moore-et-al_CT_0221_COVID19-Vaccine-Breakthrough-Recommendations.pdf
DOI: 10.5064/f6g2petf/aaegkd
title: Moore-et-al_CT_0521_Executive-Order-No-12.pdf
DOI: 10.5064/f6g2petf/n6q1jj
title: Moore-et-al_CT_0121_Governor Lamont Warns Connecticut Residents To Be Aware of COVID-19 Vaccination Scams and Report Suspicious Beha.pdf
DOI: 10.5064/f6g2petf/1ocs4n
title: Moore-et-al_CT_0421_Travel Advisory for Connecticut During the COVID-19 Pandemic.pdf
DOI: 10.5064/f6g2petf/bfdskt
title: Moore-et-al_CT_0921_Statement From Connecticut Department of Public Health Commissioner Dr Manisha Juthani.pdf
DOI: 10.5064/f6g2petf/hcrvs9
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/jqbdyt
title: Moore-et-al_CT_0921_CTDPHCOVID19summary9092021.pdf
DOI: 10.5064/f6g2petf/kdtl8i
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/fgkabs
title: Moore-et-al_CT_0821_Connecticut DPH Reminder to Parents to Make Sure Child Vaccinations Are Up To Date.pdf
DOI: 10.5064/f6g2petf/8buhnt
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/1jnvoc
title: Moore-et-al_CT_0521_CTDOTs CT In Motion Webinar Examines the Impact of COVID-19 on Workplace Trends and Commuting.pdf
DOI: 10.5064/f6g2petf/dq3nz6
title: Moore-et-al_CT_0821_Connecticut DPH Issues Health Alert Middlesex County Now Upgraded To The High Transmission Category.pdf
DOI: 10.5064/f6g2petf/bh0t9q
title: Moore-et-al_CT_0621_CVP-Pediatric-Recommendation-for-COVID-6121.pdf
DOI: 10.5064/f6g2petf/aiomdo
title: Moore-et-al_CT_1220_Governor Lamont Announces Connecticut Receives Federal Extension of Connecticut National Guard’s COVID-19 Suppor.pdf
DOI: 10.5064/f6g2petf/9pb532
title: Moore-et-al_CT_0121_Governor Lamont Extends Connecticut’s State of Emergency for the COVID-19 Pandemic To April 20.pdf
DOI: 10.5064/f6g2petf/etf4qe
title: Moore-et-al_CT_0321_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_08.pdf
DOI: 10.5064/f6g2petf/5ozeka
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_10.pdf
DOI: 10.5064/f6g2petf/j0yczr
title: Moore-et-al_CT_0321_Transportation.pdf
DOI: 10.5064/f6g2petf/jwgtku
title: Moore-et-al_CT_0221_Health Information and Advisories.pdf
DOI: 10.5064/f6g2petf/0vzbhv
title: Moore-et-al_CT_0821_CTDPHCOVID19summary8122021.pdf
DOI: 10.5064/f6g2petf/m1i0hg
title: Moore-et-al_CT_0321_Use of Commuter Parking Facilities.pdf
DOI: 10.5064/f6g2petf/qouuns
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_08.pdf
DOI: 10.5064/f6g2petf/jwbmpz
title: Moore-et-al_CT_0821_Governor Lamont Issues Executive Order Allowing Municipalities To Implement Universal Mask Requirements, Announc.pdf
DOI: 10.5064/f6g2petf/rbbj9e
title: Moore-et-al_CT_0621_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_05.pdf
DOI: 10.5064/f6g2petf/ung3db
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.5064/f6g2petf/atbcw8
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/msjnfc
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_12.pdf
DOI: 10.5064/f6g2petf/8ygl9h
title: Moore-et-al_CT_0821_Connecticut DPH Issues Health Alert Fairfield County Now Upgraded To The High Transmission Category.pdf
DOI: 10.5064/f6g2petf/8scred
title: Moore-et-al_CT_0521_What is the Get Vaccinated CT door-to-door canvassing campaign_.pdf
DOI: 10.5064/f6g2petf/y3yhyt
title: Moore-et-al_CT_0221_Governor Lamont Announces Connecticut Residents Over 65 Can Register for COVID-19 Vaccination Appointments Start.pdf
DOI: 10.5064/f6g2petf/ldoox1
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/mcliyj
title: Moore-et-al_CT_0721_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_02.pdf
DOI: 10.5064/f6g2petf/arqgu1
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_04.pdf
DOI: 10.5064/f6g2petf/6qx4be
title: Moore-et-al_CT_0921_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_11.pdf
DOI: 10.5064/f6g2petf/qmyfgw
title: Moore-et-al_CT_0421_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_10.pdf
DOI: 10.57783/vf21-z549
title: Oregon HCUP
DOI: 10.5064/f6g2petf/8fnrfv
title: Moore-et-al_CT_0521_Employment_and_Day_Provider_guidance_FINAL_5_27_21.pdf
DOI: 10.57783/zdhz-aa97
title: Oregon HCUP
DOI: 10.57783/hx9w-nh60
title: Indiana HCUP
DOI: 10.5064/f6g2petf/rrif8h
title: Moore-et-al_CT_0521_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_07.pdf
DOI: 10.57783/35s3-j229
title: New York HCUP
DOI: 10.5064/f6g2petf/gezyrx
title: Moore-et-al_CT_0721_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_03.pdf
DOI: 10.5064/f6g2petf/busda7
title: Moore-et-al_CT_0421_I Lost My Vaccine Card Can I Get a Replacement_.pdf
DOI: 10.5064/f6g2petf/4n80t7
title: Moore-et-al_CT_1220_CDC-COVID-19-Vaccine-Communication-Update-12_13.pdf
DOI: 10.5064/f6g2petf/twk3bl
title: Moore-et-al_CT_0821_Governor Lamont Announces Connecticut Implementing CDC Recommendations on Additional COVID-19 Vaccine Doses for .pdf
DOI: 10.5064/f6g2petf/mtfayh
title: Moore-et-al_CT_0821_Executive-Order-No-13B.pdf
DOI: 10.5064/f6g2petf/v167yv
title: Moore-et-al_CT_0821_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_08.pdf
DOI: 10.5064/f6g2petf/yibneo
title: Moore-et-al_CT_0921_Which contractors does the vaccine mandate apply to_.pdf
DOI: 10.5064/f6g2petf/nd65io
title: Moore-et-al_CT_0921_Are contractors required to pay for individuals' vaccination or testing costs_.pdf
DOI: 10.5064/f6g2petf/q4hgbh
title: Moore-et-al_CT_0621_Governor Lamont Announces More Than 1,000 Tenants and Landlords Have Utilized Connecticut’s COVID-19 Emergency R.pdf
DOI: 10.5064/f6g2petf/w9vm49
title: Moore-et-al_CT_0221_COVID-19 Vaccinations Education and Childcare Eligibility.pdf
DOI: 10.5064/f6g2petf/nwgztm
title: Moore-et-al_CT_0421_ProviderLetter.pdf
DOI: 10.5064/f6g2petf/gelhnb
title: Moore-et-al_CT_0321_Governor Lamont Announces Plans To Ease Some COVID-19 Restrictions in Connecticut.pdf
DOI: 10.5064/f6g2petf/odcxrm
title: Moore-et-al_CT_0721_CTDPHCOVID19summary7292021.pdf
DOI: 10.5064/f6g2petf/clahdi
title: Moore-et-al_CT_0421_CTDPH Statement on Pause In the Use of J and J Vaccine.pdf
DOI: 10.5064/f6g2petf/fn6z23
title: Moore-et-al_CT_0121_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_08.pdf
DOI: 10.5064/f6g2petf/t7vsfv
title: Moore-et-al_CT_0221_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_08.pdf
DOI: 10.5064/f6g2petf/qfryfe
title: Moore-et-al_CT_1220_Governor Lamont Provides Update on Connecticut’s Coronavirus Response Efforts_06.pdf
DOI: 10.5064/f6g2petf/udjiam
title: Moore-et-al_CT_0721_CTDPHCOVID19summary7082021.pdf
DOI: 10.5281/zenodo.17691439
title: proBait - Tutorials

description: This dataset contains the data files used in the proBait tutorials. proBait is a bioinformatics tool for designing capture probes/baits used in target capture experiments. proBait is open-source software that is freely available on GitHub. There are three tutorials, each representing a specific use case.

Spneumo

The objective of this tutorial is to demonstrate how to generate a set of baits/probes to capture the diversity of a bacterial species. In this tutorial, all the complete genomes of Streptococcus pneumoniae available on NCBI RefSeq, as of 22/11/2025, were downloaded to select a representative set of genomes for bait/probe design. The Sequence Type (ST) of each genome was determined with the MLST tool to select a representative genome per distinct ST, ending up with a dataset containing 119 complete genomes (from a total of 258 complete genomes that were initially downloaded). The 119 complete genomes were given as input to proBait to generate a set of 47,937 baits/probes. This dataset includes the genomes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait.

Multispecies

This tutorial demonstrates how to create a set of baits/probes to capture multiple bacterial species. In this case, we focused on Streptococcus pneumoniae and Streptococcus pyogenes. The dataset includes two genomes for each of the two species, one reference genome for the species, and a complete genome representative of a specific lineage to simulate a scenario where there is interest in optimizing capturing efficiency for particular strains (e.g. belonging to emerging lineages). The four complete genomes were given as input to proBait to generate a set of 33,690 baits/probes. This dataset includes the genomes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait.

MEGARes

The inputs for bait/probe set design do not have to be genome assemblies. The target DNA sequences can be anything as long as they are provided in FASTA format. In this tutorial, proBait is used to design a set of baits/probes to capture a collection of target genes, more particularly, the representative sequences for each of the 58 classes of the MEGARes database. The FASTA files containing the representative sequences for each class were given as input to proBait to generate a set of 46,561 baits/probes. This dataset includes the FASTA files containing the representative sequence for the MEGARes classes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait.
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