This document provides statistics on sequence counts and authority document counts in GenomeQuest's sequence databases. The USA, EPO, and WIPO have the largest document and sequence counts. GenomeQuest offers two database tiers: Gold+ includes sequences from major patent offices, while Platinum adds sequences from additional authorities and countries. Platinum also provides additional features such as PDF downloads and family portrait reports.

1. Sequence Search/Comparison/Analysis
Stephen Allen- Solutions Consultant

2. Authority Document Count Sequence Count Database
USA 320,873 215,305,722 Gold+
EPO 108,362 37,883,488 Gold+
WIPO 144,292 74,293,342 Gold+
Japan 104,108 27,355,841 Gold+
China 78,683 1,029,562 Platinum
India 6,446 69,071 Platinum
Canada 57,671 24,026,839 Gold+
Brazil 2,134 39,001 Platinum
Others 81,148 3,913,808 Gold+
Total 903,717 383,916,674
Country Coverage
World’s Largest Sequence Database
https://www.gqlifesciences.com/genomequest/capabilities-features/

3. GQ Gold+ vs Platinum
Topic Gold+ PLATINUM
Traditional All Patents ST.25 Listings From US, EPO, WIPO,
Korea, Japan
All Patents ST.25 Listings From US, EPO, WIPO,
Korea, Japan
Traditional
and Manual
Curation
GQ-Pat Sequences (including non-ST.25) from
US, EPO, WIPO, Korea, Japan plus the following
Authorities: AT, AU, BE, CA, CH, DE, ES, FR, GB,
LU, NL, NO, TW
GQ-Pat Sequences (including non-ST.25) from
US, EPO, WIPO, Korea, Japan plus the following
Authorities: AT, AU, BE, CA, CH, DE, ES, FR, GB,
LU, NL, NO, TW
 BRIC Country Documents: CN, BR, IN, RU +
Emerging Country Documents
Features Extended Legal Status (ELS) Extended Legal Status (ELS)
Normalized Patent Assignee; Parent Normalized Patent Assignee; Parent
Unique Family Sequence (UFS) Unique Family Sequence (UFS)
 Access to PDF Downloads
 Family Portrait Report

5. Results

6. Results Pre & Post filtering
560K sequences 2K sequencesFilter

7. Getting to Your Results
 ALGORITHMS
• Searches can be done in a broad inclusive manner by
selecting the correct algorithm and a few basic settings
 FILTERS
• Broad searches can be narrowed quickly based on
homology data, legal status, and many other critera
 VIEWS
• Views allow you to tailor the display to your liking – with
specific columns and intelligent grouping

8. Search Setup
https://www.gqlifesciences.com/blog/category/genepast/

9. Filters
• Filter your search based on specific legal status,
homology, authority, or many other categories
• Save your favorite – frequently used filters
• Save multiple filters– different filters for different searches
• Filters are categorized for fast access
• Categories include alignment properties, subject text, subject dates, subject
properties etc.
• Filters reduce reported hits based on your criteria

10. Views & Grouping
• Choose how to display your data on Results page
• Tailored views are also used for Excel Table Export
• Add Columns to View with Display List
• Display fields are similar to filter fields
• Display categories similar to filter categories
• Save favorite – frequently used views
• Save multiple views – different views for different searches
• Group based on specific criteria
• Patent ID, Patent Family, Patent Assignee
• Display all records in group, or subset for streamlined analysis

11. Details and Alignments

12. LifeQuest
Consolidated Sequence & Text Searching

13. Filter with LQ markup
Filter by Stars Filter by Color

14. • Sequence Search
• Filter
• Export Results to LQ
• Mark to distinguish sequence searches
• LQ text search
• ( ttl_abst_clm:IL-17*^5 OR ttl_abst_clm:IL17*^5) AND antibod*)
• Mark to distinguish text search
• Unite!
• Filter
• Highlight key hits
• Export
• Filter within Excel
Sample Workflow

15. Non Sequence IP

16. Claims & Alignments
Quickly add columns

17. Post Filtering
Post Filter sequence searches, text searches, or combined searches

18. Additional Linkouts

19. Contact us at:
Stephen.Allen@aptean.com
Ellen.Sherin@aptean.com
Bill Perkins@Aptean.com
Questions?

20. LifeQuest
• Unite Sequence Based & Text Based Searches
• Create Virtual Sequence Database from LQ Results

21. Nested – Savable Filters
Complex Boolean filters
• Nested filters for fine tuning
• Save standard filters for easy application

22. Alerts: See what’s new

23. Contact us at:
Stephen.Allen@aptean.com
Ellen.Sherin@aptean.com
Bill Perkins@Aptean.com
Questions?

24. Supplementary Slides
Please contact stephen.allen@aptean.com with any questions

26. Q:
S:
LOCAL ALIGNMENT
Part of the Query matches part of the
Subject. BLAST, FASTA, and Smith &
Waterman.
S:
Q: GLOBAL ALIGNMENT
All of the Query matches all of the
Subject. Needleman & Wunsch and
algorithms like it.
Q:
S:
BEST FIT ALIGNMENT
All of the Query is fitted into the
Subject. GenePast. Ideal for patent
sequence searching.
Alignment Types

27. Alignment Subject % ID Query % ID
Subject %
Coverage
Query %
Coverage
100% 100% 100% 100%
100% 50% 100% 50%
50% 100% 50% 100%
50% 50% 50% 50%
95% 95% 100% 100%
Alignment % identity, corrected for the ratio of the alignment length to either the query or subject length.
Query/Subject % Identity Definition
This example assumes 100% alignment identity, the longer lines are 100 residues, the shorter lines are 50 residues.
• By filtering for 100% subject coverage you can capture CDR to CDR matches
• With variability % ID can drop, so % coverage is the preferable filter
• This is a key feature to understand – these filters are very powerful
5 mismatches

28. Key Fields
Legal Status
Extended Legal Status And National Phase Legal Status
US PAIR Legal Status
• PAIR Legal status – Updates from US PAIR occur Monthly
Live Links to Reports, Alignments
• Links on analysis page carry over to Excel Reports
• Simple Easy Sharing among groups
Microsoft Excel 97
- 2004 Worksheet

29. Short sequences need GenePAST or Motif
searches (BLAST may miss patents)
• For short Query sequences – or for
easy analysis of variants, GenePAST
is the preferred algorithm.

30. MOTIF on full length – Direct Strike
The long sequence gives hits comprising all three CDRs in the specific order
provided. *. Represents “any number of unspecified residues, including zero”.
Motif searches require 100% match in “defined” residues.
>37-motif
DLSIH.*GFDPQDGETIYAQKFQG.*GSSSSWFDP
>9-motif
RASQGISSWLA.*GASNLES.*QQANSFPWT

31. Unique Family Sequence UFS
• Merge all identical sequences within a family
• Based on strict criteria: identical sequence, patent family, sequence length
• Examine a sequence’s status across authorities
• Group By UFS can replace group by family for finer resolution of unique hits
• UFS Identifier = MD5Sum + Sequence Length + Family ID
• UFS IDs can be transient
Normalized Sequence/Patent Family

32. Methodology – Searching CDRs
All3CDRs(orprimer/ampliconsets)insubjectorpatent
MOTIF – exact match
GenePAST – variations
By requiring a group size equal to three in the post search grouping – we show patents that
contain all three CDRs
• Fasta sequences for your search
allows multiple queries at once
• GenePAST will allow you to view
patent hits with variability in the CDRs

33. Conservative Substitutions
Subjectscomprisingall3CDRS
Upto1substitution
Subject and Query Gaps
• Gaps in CDRs and primers can be ignored
using the Query/Subject gap filter
• Variations – i.e. number of differences can
be adjusted without calculating % identity

34. Database Selection
Tree Structure and Virtual Databases
• Tree structure allows easy database search setup
• Multiple virtual databases can be chosen
• Virtual databases can be shared among teams
• Save your own databases from
keyword or IP searches – and
search within results

35. Patent Statistics Report
• For multiple queries
quickly display patents
that contain all or a
subset of the queries