User Manual

Top level concepts Searching sequence databases Running workflows

Overall layout Launching workflows Workflow results Folders Sharing Universal Search Account Settings

Use cases Opening the Sequence Database Browser Getting oriented Viewing patent annotation

Patent annotation tab Subject annotation tab Sequence tab Report data issue tab

Filtering Grouping Sorting Other functions

Virtual databases View Toggle Views Exporting Add-on applications

Use cases Opening up the Result Browser Getting oriented Viewing patent annotation

Patent annotation tab Subject annotation tab Subject sequence tab Query sequence tab Report data issue tab

Understanding alignments

Alignment statistics Alignment coloring GQ-style vs. NCBI-style alignments

Filtering Grouping Sorting Sharing Other functions

Views Workspaces Exporting

to a document to a keyword search tool to LifeQuest to a Family Portrait

Add-on applications

Example use cases Launching the IP workflow

Query sequence input Search strategy Subject database selection

Default subject databases Other subject databases Virtual databases Prefiltering subject databases

Viewing results

The report The result browser

Redoing searches Setting up alerts Saving templates

Launching the Keyword Search tool Types of keyword searches

Patent Number (PN) search Global search

Other ways to browse databases

Example use cases Launching the BLAST workflow

Query sequence input Subject database selection Search strategy Other options

Viewing results Differences between this workflow
and the IP workflow Limits on sequence search

Use cases Launching the analysis Exploring the results

Overview Grouping Options Sort Results Charts Annotations Multiple Query Sequence Analysis Variation Filters Views Highlight Text Search Result Set GQ Power Tools Export Results

Variation Filter Variation Landscape Report Launch Variation Module Search Variation Filter Options Query Sequence and Filter Cover Variation Filter Logic Multi-Annotation - Mark and Filter Annotate Multiple Records Variation Filter Examples Variation Landscape Report Multiple Filters Global Filters

Antibody Search Launch Page Antibody Report Interacting with Antibody Data New Report Generation Current Limitations

Full text Search Page Query Syntax Booleans, Grouping, Phrase Searching Wildcard Operators Ontologies and Your Word Lists Constraining Searches to Specific Fields

Content Updates Release Notes

Overview of offerings GQ-Pat Gold+

Automated Entries

Data sources Timeliness Quality control

GQ-Pat Platinum

Platinum countries Free PDFs Family Portrait

Manual Curation GQ-Pat Details

Patent number formats Normalized patent assignee Normalized parent Unique Family Sequence Legal statuses

Legal status Extended legal status Legal status - national phase US PAIR legal status

GQ-Pat Field list

Public databases CAS Biosequences™ GENESEQ Your databases Working with Multiple Databases

Raw format FASTA format EMBL format

Knowing which search strategy to use GenePAST

GenePAST by percent identity GenePAST by number of errors

BLAST

Regular BLAST Searching BLAST Searching with
special HSP handling

Fragment search Motif search Mega search

Supported Browsers Frequently Asked Questions Appendix: Legal Status and
Patent Kind Codes

Dojo dGrid dStore CujoJS Bootstrap Open Grid Scheduler / Grid Engine

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