Generating subsequence catalogs for nucleic acid synthesis

1 . A method of nucleic acid sequence synthesis, comprising:

providing at least one reference sequence;

determining a plurality of repeated subsequences included in the at least one reference sequence, individual repeated subsequences of the plurality of repeated subsequences including a plurality of bases arranged in a pattern that occurs at multiple locations of the at least one reference sequence;

generating at least one subsequence catalog that includes the plurality of repeated subsequences;

synthesizing a plurality of nucleic acid fragments based on the plurality of repeated subsequences included in the at least one subsequence catalog, the plurality of nucleic acid fragments including at least one nucleic acid fragment for the individual repeated subsequences of the plurality of repeated subsequences;

adding the plurality of nucleic acid fragments to a fragment library;

determining an order for synthesizing a nucleic acid target sequence by:

determining a first number of locations of the nucleic acid target sequence to be synthesized by determining locations of the nucleic acid target sequence that match a longest subsequence included in the fragment library; and

determining a second number of locations of the nucleic acid target sequence to be synthesized subsequent to the first number of locations by determining locations in the nucleic acid target sequence that match a next-longest subsequence included in the fragment library; and

synthesizing, according to the order, the nucleic acid target sequence using a number of fragments from the fragment library.

2 . The method of nucleic acid sequence synthesis of claim 1 , wherein generating the at least one subsequence catalog comprises the steps of:

i) providing a non-transient computer readable medium encoding the at least one reference sequence and computer-executable code; and

ii) returning a subsequence catalog to the same or alternate non-transient computer readable medium;

wherein the computer-executable code is configured to enable a computer processor operably connected to the non-transient computer readable medium to: retrieve the at least one reference sequence; apply at least one pattern-recognition algorithm to the at least one reference sequence to determine the plurality of repeated subsequences; and generate the at least one subsequence catalog.

3 . The method of nucleic acid sequence synthesis of claim 2 , wherein the at least one pattern-recognition algorithm is a compression algorithm or Lempel-Ziv-Welch compression algorithm.

4 . The method of nucleic acid sequence synthesis of claim 2 , wherein the alternate non-transient computer readable medium is operably connected with a synthesizer.

5 . The method of nucleic acid sequence synthesis of claim 2 , comprising:

applying the at least one pattern-recognition algorithm to the at least one reference sequence to determine that at least one repeated subsequence of the plurality of repeated subsequences includes a same pattern of bases repeated two or more times.

6 . The method of nucleic acid sequence synthesis of claim 2 further comprising:

subjecting the plurality of repeated subsequences to inclusion criteria;

wherein said inclusion criteria includes at least one of: subsequences that are repeated at least a threshold number of times; subsequences that meet a predetermined threshold number or percentage of repetitions in the at least one reference sequence; subsequences that repeat most frequently; repeating subsequences of at least a minimum number of bases; or subsequences that are not expected to exceed a threshold error rate during synthesis.

7 . The method of nucleic acid sequence synthesis of claim 2 , further comprising:

iii) providing the at least one subsequence catalog to an assembly planner; and

iv) directing, via the assembly planner, the synthesis of the nucleic acid target sequence;

wherein the assembly planner is configured to determine an order of assembly of the nucleic acid target sequence using the at least one subsequence catalog and the plurality of nucleic acid fragments available in the fragment library.

8 . The method of nucleic acid sequence synthesis of claim 1 , wherein the plurality of nucleic acid fragments include at least two nucleic acids.

9 . The method of nucleic acid sequence synthesis of claim 1 , wherein the at least one reference sequence is at least two sequences each from a same or a different type.

10 . The method of nucleic acid sequence synthesis of claim 1 , wherein the nucleic acid target sequence is the same or different from the at least one reference sequence.

11 . The method of nucleic acid sequence synthesis of claim 1 , wherein the nucleic acid target sequence comprises a non-identical nucleic acid sequence having a same type as the at least one reference sequence.

12 . The method of nucleic acid sequence synthesis of claim 1 , wherein the nucleic acid target sequence is synthesized according to the order by first synthesizing the first number of locations of the nucleic acid target sequence that correspond to the longest subsequence included in the fragment library and next synthesizing the second number of locations of the nucleic acid target sequence that correspond to the next-longest subsequence in the fragment library.

13 . A method of nucleic acid sequence synthesis, comprising:

providing at least one reference sequence;

determining a plurality of repeated subsequences included in the least one reference sequence, individual repeated subsequences of the plurality of repeated subsequences including a plurality of bases arranged in a pattern that occurs at multiple locations of the at least one reference sequence;

generating at least one subsequence catalog that includes the plurality of repeated subsequences;

synthesizing a plurality of nucleic acid fragments based on the plurality of repeated subsequences included in the at least one subsequence catalog, the plurality of nucleic acid fragments including at least one nucleic acid fragment for the individual repeated subsequences of the plurality of repeated subsequences;

adding the plurality of nucleic acid fragments to a fragment library;

determining an order for synthesizing a nucleic acid target sequence by:

determining a first number of locations of the nucleic acid target sequence to be synthesized by determining a longest subsequence included in the fragment library that matches a beginning portion of the nucleic acid target sequence; and

determining a second number of locations of the nucleic acid target sequence to be synthesized by determining a next-longest subsequence included in the fragment library that matches a next portion of the nucleic acid target sequence subsequent to the beginning portion; and

synthesizing, according to the order, the nucleic acid target sequence using a number of fragments from the fragment library.

14 . The method of claim 13 , wherein synthesizing the nucleic acid target sequence according to the order includes first synthesizing the longest subsequence included in the fragment library that corresponds to a beginning portion of the nucleic acid target sequence and next synthesizing the next-longest subsequence in the fragment library that corresponds to the next portion of the nucleic acid target sequence.