Methods and apparatus for performing sequence homology detection

A network-based method of detecting homologies between a plurality of sequences in a database accessed at a server in the network and a query sequence entered at a client device in the network, the method comprising the steps of:

• obtaining, at the server from the network, the query sequence entered at the client device;
• accessing, at the server, patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database;
• comparing, at the server, the query sequence to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns;
• and
• generating a score, at the server, for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score determines a degree of homology between the query sequence and the detected sequence.

Apparatus for detecting homologies between a plurality of sequences in a database and a query sequence over a network, the apparatus comprising:

• a client device configured to enter the query sequence and transmit the query sequence over the network;
• and
• a server, coupled to the client device via the network, and configured to:
• (i) obtain the query sequence from the client device over the network;
• (ii) access patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database;
• (iii) compare the query sequence to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns;
• (iv) generate a score for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score determines a degree of homology between the query sequence and the detected sequence;
• and (v) transmit at least a portion of the detection results to the client device over the network.

Apparatus for detecting homologies between a plurality of sequences in a database and a query sequence, the apparatus comprising:

• at least one processor operative to:
• (i) access patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database;
• (ii) compare the query sequence to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns;
• and (iii) generate a score for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score determines a degree of homology between the query sequence and the detected sequence.

An article of manufacture for detecting homologies between a plurality of sequences in a database and a query sequence, comprising a machine readable medium containing one or more programs which when executed implement the steps of:

• accessing patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database;
• comparing the query sequence to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns;
• and
• generating a score for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score determines a degree of homology between the query sequence and the detected sequence.

A computer-based method of detecting homologies between a plurality of sequences in a database and a query sequence, the method comprising the steps of:

• accessing patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database;
• comparing the accessed patterns to the query sequence to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the accessed patterns;
• and
• generating a score for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score represents a degree of homology between the query sequence and the detected sequence.

A computer-based method of detecting homologies between a plurality of sequences in a database and a query sequence, the method comprising the steps of:

• accessing patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database, wherein at least a portion of the patterns each have a variable length associated therewith and wherein, for one or more positions in the pattern, a nature or an identity of a corresponding portion of a sequence is unspecified;
• comparing the query sequence and the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns;
• and
• generating a score for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score represents a degree of homology between the query sequence and the detected sequence.