Example BoaG Programs
BoaG is a flexible language, capable of answering a wide variety of questions. Here we provide several example questions and BoaG programs to answer those questions.
- What are proteins in the NR database that have taxonomic name "Escherichia coli"?
- What are the list of conserved proteins?
- What are protein sequences and the frequencies of coronavirus in taxonomic assignments?
- What is the frequency of protein length in the NR database?
- What are all clusters belong to a specific protein function SCN?
- What are number of protiens in each phylum in the tree of life?
- What are the list of taxonomic assignment for all proteins in NR?
- How many proteins in NR do not have a taxonomic assignment?
What are proteins in the NR database that have taxonomic name "Escherichia coli"?
s: Sequence = input;
count : output sum[string] of int;
foreach(i:int; def(s.annotation[i]))
if (strfind( "Escherichia coli", s.annotation[i].tax_name) > -1)
count[s.seqid] << 1;
Run Example | Published Results
What are the list of conserved proteins?
s: Sequence = input;
protOut : output sum [string][string] of int;
distinctTax := function (seq: Sequence): int{
taxSet : set of string;
foreach(i:int; def(seq.annotation[i]))
add(taxSet,seq.annotation[i].tax_id);
return(len(taxSet));
};
# we define conserved proteins as those who have > 10 distinct taxonomic assignments
if (distinctTax(s) > 10){
foreach(i:int; def(s.annotation[i])){
if (strfind("[",s.annotation[i].defline)> 0)
protOut [trim(substring(s.annotation[i].defline, 0, strfind("[",s.annotation[i].defline)))][s.seqid] << 1;
else
protOut [s.annotation[i].defline][s.seqid]<<1;
}
}
Run Example | Published Results
What are protein sequences and the frequencies of coronavirus in taxonomic assignments?
s: Sequence = input;
count : output sum[string][string] of int;
foreach(i:int; def(s.annotation[i]))
if (strfind( "coronavirus", s.annotation[i].tax_name) > -1)
count[s.seqid][s.annotation[i].tax_name] << 1;
Run Example | Published Results
What is the frequency of protein length in the NR database?
s: Sequence = input;
counts: output sum[int] of int;
foreach(i:int; def(s.cluster[i]))
if (s.cluster[i].similarity==95)
counts [s.cluster[i].length] << 1;
Run Example | Published Results
What are all clusters belong to a specific protein function SCN?
s: Sequence = input;
counts_protein: output collection[string][string] of int;
foreach(i:int; def(s.cluster[i]))
if (s.cluster[i].similarity==95)
if (strfind( "SCN", s.annotation[i].defline) > -1)
counts_protein [s.seqid][s.cluster[i].cid] << 1;
Run Example | Published Results
What are number of protiens in each phylum in the tree of life?
# search for Streptococcus
s: Sequence = input;
phylCount: output sum [string] of int;
taxs := {"Firmicutes", "Fusobacteria"};
for (j := 0; j < len(taxs); j++)
exists (i: int; match(taxs[j], s.annotation[i].tax_name))
phylCount[taxs[j]] << 1;
Run Example | Published Results
What are the list of taxonomic assignment for all proteins in NR?
s: Sequence = input;
clstrOut : output collection [string] of string;
getTaxList := function(seq: Sequence):string {
taxids :="";
foreach(i:int; def(s.annotation[i])){
if (s.annotation[i].tax_name !="")
taxids = taxids + s.annotation[i].tax_id + " ";}
return taxids ;
};
foreach(i:int; def(s.cluster[i]))
if (s.cluster[i].similarity==95 && s.cluster[i].representative)
clstrOut [s.seqid] << getTaxList(s);
Run Example | Published Results
How many proteins in NR do not have a taxonomic assignment?
s: Sequence = input;
countNull: output sum of int;
foreach (i: int; def(s.annotation[i]))
if (s.annotation[i].tax_name == "")
countNull << 1;
