Relational database and system for storing information relating to biomolecular sequences and reagents

A computer system, comprising:

• a relational database having
• (i) records containing information identifying sequences with associated information from a relational gene sequence database,
• (ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said gene sequence database based on specified priority criteria, and
• (iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;
• and
• a user interface allowing a user to selectively access the information contained in the records.

A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:

• providing a relational database having
• (i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and
• (ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;
• entering, in a graphical user interface, a query relating to the information contained in the records;
• determining matches between said query entry and said information;
• and
• displaying the results of said determination.

A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:

• providing a relational database having
• (i) records containing information identifying sequences with associated information from a relational gene sequence database,
• (ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said relational gene sequence database based on specified priority criteria, and
• (iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;
• entering, in a graphical user interface, a query relating to the information contained in the records;
• determining matches between said query entry and said information;
• and
• displaying the results of said determination.

A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having

• (i) records containing information identifying sequences of a plurality of reagent clones, wherein said reagent clones have been nominated based on specified priority criteria, and
• (ii) records containing information identifying reagent information accumulated in sequencing and verification of said plurality of reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;
• the computer program product comprising computer-readable program code for effecting the following steps within a computing system:
• providing an interface for receiving a query relating to the information contained in the records;
• determining matches between said query entry and said information;
• and
• displaying the results of said determination.

A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having

• (i) records containing information identifying sequences with associated information from a relational gene sequence database,
• (ii) records containing information identifying sequences of a plurality of reagent clones that have been nominated from said relational gene sequence database based on specified priority criteria, and
• (iii) records containing information identifying reagent information accumulated in sequencing and verification of said reagent clones, wherein verification comprises using laboratory processes to verify that said plurality of reagent clones is viable;
• the computer program product comprising computer-readable program code for effecting the following steps within a computing system:
• providing an interface for receiving query relating to the information contained in the records;
• determining matches between said query entry and said information;
• and
• displaying the results of said determination.

A method, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:

• grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster;
• assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships of sequences to each other in the master cluster are elucidated;
• nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria and verifying the quality of the reagent clone by laboratory processes, wherein said laboratory processes comprise verifying that the reagent clone is viable and can grow to amounts suitable for isolating the clone's polynucleotide insert sequence;
• and
• sequencing said clone's polynucleotide insert sequence using 5′ and 3′ long read sequencing,
• wherein said priority criteria comprise:
• (1) a clone associated with a 5′-most initial sequence in an assembly;
• (2) a clone having an insert in a pINCY vector, such that if the 5′-most clone in the assembly is not a pINCY clone, the 5′-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′-most clone;
• and
• (3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.

A reagent clone identified by a process, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:

• grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster;
• assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships or sequences to each other in the master cluster are elucidated;
• and
• nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria wherein said priority criteria comprise:
• (1) a clone associated with a 5′-most initial sequence in an assembly;
• (2) a clone having an insert in a pINCY vector, such that is the 5′-most clone in the assembly is not a pINCY clone, the 5′-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′-most clone;
• and
• (3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.