GenomeQuest 7.2 is full of many new and exciting one-of-a-kind features

Contents 1 Annotation 1.1 Annotation Engine 1.2 Annotation Data Sources 1.3 Annotation Filtering 2 GenomeQuest Alignment Engine 3 User Interface 3.1 Layout 3.2 Data Formats

Annotation

Annotation Engine

• Completely re-written turbo-charged annotation engine! Annotate a whole genome in minutes!
• Brand new gene model produces the most accurate representation of the NCBI gene model - annotates variants in Genes, CDS, Repeats, Splice Sites, Exons, UTR's.
• Re-written and improved mutation protein impact prediction - find impacts like deletions, insertions, frameshift, stops, damaging stops, premature stops, silent, substitutions.
• HGVS Nomenclature compliant output.
• Handles mitochondrial genome specificities

Annotation Data Sources

• HGMD (Human Gene Mutation Database) has been added as an annotation track. ^†
• The latest dbSNP135 available for Human (hg19)
• The latest dbSNP132 for Mouse (mm9)
• SIFT (hg19) protein impact prediction annotation track added. Predicts whether amino acid substitutions in a protein will have a phenotypic effect.
• Polyphen-2 (hg19) protein impact prediction annotation track added. Predict amino acid substitution on the structure and function of a human protein.

^† Subscription required for use.

Annotation Filtering

• The world's most powerful variant enrichment interface
• Interrogate your variant information using 70+ different criteria compiled from the world's genomic knowledge
• Use the filtering panel to focus in on those variants of interest to you.

GenomeQuest Alignment Engine

• World's first algorithm to detect small to medium indels (up to 50 bp) in your sample on a Whole Genome Scale
• Read mapping is now 5x faster! Map a whole human genome equivalent in one hour!
• Native support of BAM files with the ability to export and download
• Advanced Paired End support

User Interface

Layout

• New, more intuitive menu layout
• Redesigned welcome screen that mirrors the new menu layout, showing both recent samples added and recent analyses
• New ability to quickly merge databases to perform operations on pooled samples or combine samples from different sequencing runs.
• New quality chart showing your sample's sequence quality by base

Data Formats

• Support for Ion Torrent data has been added
• You can now import your own reference sequences and genomes to GQ and align your reads against it.
• SAM/BAM import support added, we now support the ability to import your own external mapping results.