Molecular standards for microbial pathogens
A method for constructing a consensus sequence from a sequence alignment. The consensus sequence may be used to generate molecular standards that may substitute for genomic DNA in various assays. Since a molecular standard cannot have unresolved bases, the method removes less informative sequences to resolve all positions in the alignment. Also includes several sequences from pathogenic waterborne species that were constructed according to the method.
1. A method for constructing a consensus sequence from an alignment of a plurality of nucleic acid sequences, the method comprising:
generating a frequency matrix comprising the frequency of each base at each position in the alignment;
creating an information matrix comprising the amount of information provided by each base at each position in the alignment; and
calculating an information score for each of the plurality of nucleic acid sequences;
iterating over each position in the alignment and for each position:
(a) calculating base frequencies and determining a highest frequency base;
(b) if the highest frequency base's frequency is higher than a frequency threshold, assigning the highest frequency base to the consensus sequence; and
(c) if the highest frequency base's frequency is lower than the frequency threshold, removing a base corresponding to a nucleic acid sequence with a lowest information score and returning to (a); and
performing a restriction fragment length polymorphism (RFLP) fingerprint of the constructed consensus sequence in silico.
2. The method of claim 1 , further comprising removing insertions and deletions from the alignment of a plurality of nucleic acid sequences.
3. The method of claim 1 , wherein
creating an information matrix comprises calculating the decrease in Shannon uncertainty for each base at each position in the alignment; and
calculating an information score comprises summing the decrease in Shannon uncertainty for each base in each of the plurality of nucleic acid sequences.
4. The method of claim 1 , further comprising:
comparing a restriction fragment length polymorphism (RFLP) fingerprint of the constructed consensus sequence to a RFLP fingerprint of each of the plurality of nucleic acid sequences in the alignment;
determining an oligonucleotide to bind to the consensus sequence; and
comparing the oligonucleotide binding to the constructed consensus sequence and to the plurality of nucleic acid sequences in the alignment based on at least one of a Gibb's free energy of hybridization, a melting temperature, and a binding position.
5. The method of claim 1 , wherein the frequency threshold is 0.7.
6. A method for constructing a consensus sequence from an alignment of a plurality of nucleic acid sequences, the alignment comprising a plurality of alignment positions, the method comprising:
determining the plurality of nucleic acid sequences from a computer database;
generating a frequency matrix comprising the frequency of each base at each alignment position;
creating an information matrix comprising the amount of information provided by each base at each alignment position;
calculating an information score for each of the plurality of nucleic acid sequences; and
iterating over the alignment and for each alignment position:
(a) determining a highest frequency base;
(b) if the highest frequency base's frequency is higher than a frequency threshold, assigning the highest frequency base to the consensus sequence;
(c) if the highest frequency base's frequency is lower than the frequency threshold, removing from the current alignment position a base corresponding to a nucleic acid sequence with a lowest information score, recalculating base frequencies for the current alignment position, and returning to (a); and
performing a restriction fragment length polymorphism (RFLP) fingerprint of the constructed consensus sequence in silico.
7. The method of claim 6 , further comprising removing insertions and deletions from the alignment of a plurality of nucleic acid sequences.
8. The method of claim 6 , further comprising:
comparing a restriction fragment length polymorphism (RFLP) fingerprint of the constructed consensus sequence to a RFLP fingerprint of each of the plurality of nucleic acid sequences in the alignment; and
comparing oligonucleotide binding to the constructed consensus sequence and to the plurality of nucleic acid sequences in the alignment based on at least one of a Gibb's free energy of hybridization, a melting temperature, and a binding position.
9. The method of claim 6 , wherein
creating an information matrix comprises calculating the decrease in Shannon uncertainty for each base at each position in the alignment; and
calculating an information score comprises summing the decrease in Shannon uncertainty for each base in each of the plurality of nucleic acid sequences.
10. The method of claim 6 , wherein the frequency threshold is 0.7.