SequenceBase is pleased to announce Beta release of our Multiple Sequences Search (MSS) tool, which represents a significant technological breakthrough and introduces unique capabilities to the Research Portal users. MSS is a general purpose tool, which can be used for applications, such as searching for complementarity determining regions (CDRs), fusion/chimeric constructs, recombinant plasmid constructs and bispecific antibodies, and it supports both protein and nucleotide searches.
To illustrate, using CDR research as an example, a Research Portal user could use the MSS tool to find and list documents that contain CDR sequences of interest, and one may also perform a simultaneous search on multiple CDRs contained within the same patent document, taking into consideration that the CDRs might be present in different claims.
The MSS tool uses the Smith-Waterman algorithm in order to produce highly accurate and comprehensive results. The results are ranked by patent document and the number of sequences by patent that match the queries. The interface makes it easy to track and see whether there is one or more than one similar sequence that might have been claimed within a single document.
The following example illustrates a CDR search where CDR1(Q1), CDR2(Q2) and CDR3(Q3) are present in one sequence (6132722.20):
Please note that the system provides an option to show combined alignment for such cases.
A somewhat different example illustrates a patent document with CDR1(Q1), CDR2(Q2) and CDR3(Q3) present in 4 different sequences within one patent. In this example, CDR1(Q1) and CDR3(Q3) are both present in the same sequence SEQ ID NO 160 (and in SEQ ID NO 172) while CDR2(Q2) is represented in separate sequences within the patent.
Please note that it’s possible to recover (include in the results) those documents that lack matches to one or more of the query sequences. For example, those documents that might display only CDR1(Q1) and CDR3(Q3), but not CDR2(Q2) similar sequences:
An advanced scoring system was designed to assign a higher score to those documents that contain a greater number of CDRs matching the search query, which produces more relevant results.
The Multiple Sequences Search tool can accept and search on up to six (6) query sequences. Each sequence can be simultaneously queried against any combination of the databases covered by your subscription (GENESEQ, FASTAlert, USGENE, WOGENE and GENBANK).
The new Multiple Sequences Search offering was designed to bring a higher degree of sophistication and power to the existing and future SequenceBase customers. If you are not yet a SequenceBase Research Portal subscriber, please contact SequenceBase to arrange for a free trial, and should you find new and different uses for the Multiple Sequences Search function, we’d love to hear your story.