Welcome to the GenomeQuest Documentation Wiki
What is GenomeQuest?
GenomeQuest is THE biological sequence data management platform for:
- Analyzing data from next generation sequencing technologies.
- Analyzing patent landscapes around sequences.
The best way to get specific answers to your questions is to send them by email to firstname.lastname@example.org.
- My GenomeQuest IP: Your home page on GenomeQuest for the IP version; it has all of your databases and results.
- My GenomeQuest NGS: Your home page on GenomeQuest for the Next Generation Sequencing version of GenomeQuest; it has all of your databases and results.
- File Upload: How to upload files containing your NGS reads, variants or reference databases.
- Top Level Menu items: Get information on results, launch applications, create reports.
- Filtering Widget: How to remove results you don't want from the view.
- Grouping Widget: How to group your results in different ways.
- Using Groups and Tags: How to create groups, and use tags efficiently and effectively.
- Merging databases into a larger Virtual Database (VDB): Merge your physical sequence databases into a virtual database to analyze them together using a number of GenomeQuest workflows.
Sequence Search Help
- Sequence Search for IP users: Intellectual property sequence search.
- Sequence Search for biology users: The workflow for searching sequence(s) against database(s).
- Sequence Result Browser: How to interact with sequence comparisons.
- Sequence Database Browser: Looking up sequences by keywords.
- Align 2 Sequences: Aligning 2 sequences.
- Keyword Search Tool: Using the keyword search, and syntax.
The following NGS workflows are available in GenomeQuest.
- Annotate: Annotate your long reads or contigs against public databases.
- BLAST (Sequence Search): The biological workflow for searching sequence(s) against database(s).
- ChIP-Seq: Analyze protein interactions with genomic DNA by combining chromatin immunoprecipitation (ChIP) with NGS
- IP (Sequence Search): Intellectual property search.
- Metagenomics: The workflow for rapid annotation of reads against reference databases.
- Newbler: Assemble your NGS reads de novo using 454's Newbler Assembler.
- Preparing Reads: Workflow for post-processing of uploaded reads and quality scores.
- RNA-Seq: Analyzing NGS runs to measure differential gene expression.
- SNPs and Indels Import: Import your SNPs and Indels into GenomeQuest.
- Whole Genome Variant Caller: Identifying SNPs and indels in genomes, exomes and targeted resequencing experiments.
- Velvet: Assemble your NGS reads de novo using the Velvet Assembler.
- SAM / BAM Import - new content: Import aligned reads from SAM or BAM files into GenomeQuest's internal format through the SAM / BAM Import Workflow.
- Overview: An overview of the different ways you can extend and integrate the GenomeQuest system
- How do I...? Some key common tasks developers perform
- System Concepts: A detailed look at GenomeQuest's system-level concepts
- Reference Manual: The reference manual for our various APIs, when you want just the facts
- The URL API: A powerful API for interacting with GenomeQuest data.
- GenomeQuest Databases: Reference databases from the public domain available in GenomeQuest.
- Collated databases: Databases collated and made searchable by GenomeQuest.
- GQ-Pat: GenomeQuest's archive of sequences from patents.
- DrugBank Pro: Database of drugs, drug targets and drug metabolizing enzymes developed in collaboration with the DrugBank group.
- GQ Gene: GenomeQuest's database of genes collated from Entrez Gene, Genbank and RefSeq.
- GENESEQ: Geneseq database of sequences in patents from Thomson-Reuters.
- Your Databases: How to show your own databases in GenomeQuest. And why.
- Sequence file formats: sequence database formats are used in GenomeQuest.
- Server configuration for installing GenomeQuest: If you want to install GenomeQuest behind your firewall, please read this specification for the server needed.
- Usage Costs (over and above seat-license costs)
- Frequently Asked Questions: Questions about uploading your sequences, running workflows, sharing results and working with GenomeQuest.
- Change in URL for GenomeQuestLive! service: As of Sunday 1 August 2009, GenomeQuestLive! service is available through the new URL: https://my.genomequest.com.
- GQ Gene Viewer: How to view sequences in a gene context.
These are the updates, modifications, and revisions made in each version of GenomeQuest: