Wolfram Research

Wolfram Data Repository

Immediate Computable Access to Curated Contributed Data

Protein Sequences for the SARS-CoV-2 Coronavirus

Source Notebook

Protein sequences of the SARS-CoV-2 virus (the virus associated with the COVID-19 disease, formerly known as 2019-nCoV) including location, collection time and similar supporting data. (This data was imported and made computable at 6 am CST on February 25, 2021.)

Details

This data is imported from the National Center for Biotechnology Information (NCBI) and formatted for computation.
Properties provided with each sequence include: "Accession", "Length", "Authors", "Publications", "GeographicLocation", "DetailedGeographicLocation", "USState", "Host", "Sequence", "CollectionDate", "ReleaseDate", "InclusionDate", "GenBankTitle", "Protein", "SequenceType", "ProteinStatus", "IsolationSource" and "BioSample".
Additional content elements include:
"CollectionHistogram" a DateHistogram of when the sequences were collected
"ReleaseHistogram" a DateHistogram of when the sequences were released to the public
"InclusionHistogram" a DateHistogram of when the sequences were included in the source for this data
"AffectedLocations" a world map showing where these sequences were collected

Examples

Basic Examples

Get a Dataset containing rows for each sequence:

In[1]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus"]
Out[1]=

Return the latest date a sequence was included:

In[2]:=
ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][Max, \ "InclusionDate"]
Out[2]=

Count proteins by the reported description:

In[3]:=
ReverseSortBy[ ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus"][ Counts, "Protein"], #2]
Out[3]=

Most of these protein sequences are collected from humans, but not all:

In[4]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[Not[MissingQ[#Host]] &]][Counts, "Host"]
Out[4]=

Scope & Additional Elements

Get a date plot of collection dates:

In[5]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus", \ "CollectionHistogram"]
Out[5]=

See a data histogram of release dates:

In[6]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus", \ "ReleaseHistogram"]
Out[6]=

See a timeline plot of inclusion dates:

In[7]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus", \ "InclusionHistogram"]
Out[7]=

Show the locations where the sequences were gathered:

In[8]:=
ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus", \ "AffectedLocations"]
Out[8]=

Visualizations

Most of the provided protein sequences come from the United States and Australia:

In[9]:=
BarChart[Take[ Sort[ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[Not[MissingQ[#GeographicLocation]] &]][Counts, "GeographicLocation"]], -20], ChartLabels -> Automatic, BarOrigin -> Left, ImageSize -> 700]
Out[9]=

When we look at the geographic locations providing protein sequences with the most common title, “surface glycoprotein”, these proportions are largely maintained:

In[10]:=
BarChart[Take[ Sort[ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[ And[Not[MissingQ[#GeographicLocation]], #Protein === "surface glycoprotein"] &]][ Counts, "GeographicLocation"]], -20], ChartLabels -> Automatic, BarOrigin -> Left, ImageSize -> 700]
Out[10]=

Most of the provided sequences come from regions in the Unites States and Australia:

In[11]:=
BarChart[Take[ Sort[ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[Not[MissingQ[#DetailedGeographicLocation]] &]][Counts, "DetailedGeographicLocation"]], -20], ChartLabels -> Automatic, BarOrigin -> Left, ImageSize -> 700]
Out[11]=

When we look at the detailed geographic locations providing protein sequences with the most common title, “surface glycoprotein”, these proportions are again largely maintained:

In[12]:=
BarChart[Take[ Sort[ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[And[#Protein === "surface glycoprotein", Not[MissingQ[#DetailedGeographicLocation]]] &]][Counts, "DetailedGeographicLocation"]], -20], ChartLabels -> Automatic, BarOrigin -> Left, ImageSize -> 700]
Out[12]=

Analysis

By gathering all of the titles by their protein label, we can see that the same proteins are submitted under a wide variety of names:

In[13]:=
processProteinLabel[proteinLabel_String] := Module[{prot = proteinLabel}, If[StringStartsQ[prot, "RecName:"], prot = StringCases[prot, StartOfString ~~ "RecName: Full=" ~~ Shortest[fulltitle___] ~~ ";" | EndOfString :> StringTrim[fulltitle]][[1]] ]; StringTrim@ StringReplace[StringTrim@ToLowerCase[prot], { "membrance" -> "membrane", "2019-ncov s2 subunit,2019-ncov s2 subunit" -> "2019-ncov s2 \ subunit", "proteiin" -> "protein", ", partial" -> "", StringExpression["[", BlankNullSequence[], "]"] -> "", "-" -> "", "," -> "", StringExpression[WordBoundary, "protein", WordBoundary] -> "", "partial" -> "", StringExpression["chain ", WordCharacter, WordBoundary] -> ""}]]; refseqs = DeleteDuplicates@ ResourceData["Protein Sequences for the SARS-CoV-2 Coronavirus"][ Select[#SequenceType == "RefSeq" &], {"Protein", "Sequence"}]; Dataset[Table[ <|"NCBI Protein Label" -> s[[1]], "Submitted Names" -> DeleteDuplicatesBy[ Union[processProteinLabel /@ DeleteMissing[ Normal@ResourceData[ "Protein Sequences for the SARS-CoV-2 Coronavirus"][Select[ Or[#Protein == s[[1]], #Sequence == s[[2]]] &], "GenBankTitle"]]], ToLowerCase] |> , {s, Normal[refseqs]} ] ][ReverseSortBy[Length[#"Submitted Names"] &]]
Out[14]=

We can plot where these proteins are found along the reference SARS-CoV-2 genome. To properly find an alignment, we align the protein reference sequences with the translation of each potential frame shift and choose the best alignment:

In[15]:=
originalReferenceSequence = BioSequence["DNA", Normal[ResourceData[ "Genetic Sequences for the SARS-CoV-2 Coronavirus"][ Select[#Accession === "NC_045512" &]]][[1]]["Sequence"]]; translateDNASeqWithOffset[seq_BioSequence, offset_] := BioSequenceTranslate[ BioSequenceModify[StringDrop[seq, offset], "DropIncompleteCodons"]]; shiftTranslations = translateDNASeqWithOffset[originalReferenceSequence, #] & /@ Range[0, 2]; extractAligningRange[alignment : {__}] := Module[{workingAlignment, startCoord, endCoord}, If[MatchQ[Last[alignment], {_, ""}], workingAlignment = Most[alignment], workingAlignment = alignment ]; If[MatchQ[First[workingAlignment], {_, ""}], startCoord = StringLength[workingAlignment[[1, 1]]] + 1; workingAlignment = Rest[workingAlignment], startCoord = 1 ]; endCoord = Total[StringLength[If[StringQ[#], #, First[#]]] & /@ workingAlignment] + startCoord - 1; {startCoord, endCoord} ]; localLength[alignment_List] := Max[StringLength[StringJoin[Last /@ Select[alignment, ListQ]]], StringLength[ StringJoin[First /@ Select[alignment[[2 ;; -2]], ListQ]]]]; findAligningRangeFromTranslations[seq_] := Module[{alignments, bestShiftPos, localLengths}, alignments = SequenceAlignment[#, seq, Method -> "Local"] & /@ shiftTranslations; localLengths = localLength /@ alignments; bestShiftPos = First[Ordering[localLengths]]; If[localLengths[[bestShiftPos]]/StringLength[seq] < 0.1, ((extractAligningRange[alignments[[bestShiftPos]]] + bestShiftPos - 1)*3) - 2, None ] ]; alignmentRanges = SortBy[DeleteCases[{#[[1]], findAligningRangeFromTranslations[#[[2]]]} & /@ Values[Normal@refseqs], {_, None}], MinMax[Last[#]] &]; Column[Map[Function[{plotBatch}, NumberLinePlot[Reverse[Interval /@ plotBatch[[All, 2]]], PlotLegends -> Reverse[plotBatch[[All, 1]]], PlotRange -> {1, 29903}, ImageSize -> 400, AxesLabel -> "base pairs"] ], Partition[alignmentRanges, UpTo[8]] ]]
Out[22]=

Wolfram Research, "Protein Sequences for the SARS-CoV-2 Coronavirus" from the Wolfram Data Repository (2021) 

License Information

Public Domain

Data Resource History

  • Date Created:
  • Updated: 25 February 2021

Source Metadata

  • Title: Severe acute respiratory syndrome coronavirus 2 data hub: Search, retrieve, and analyze SARS-CoV-2 GenBank data.
  • Creator: National Center for Biotechnology Information
  • Publisher: NCBI Virus: Sequences for discovery
  • Date: 25 February 2021
  • Language: English
  • Citation:

See Also

Data Downloads

Publisher Information

  • Contributed By: John Cassel and Carlos Muñoz, Wolfram|Alpha
  • Publisher of Record: Wolfram Research