Plant and Animal Genome XXIII: Schedule of the NCBI Exhibit Booth, Presentations, Posters and Workshop
PAGXIII Conference Website
Location: Town and Country Hotel, San Diego, California USA
January 10-14, 2015
NCBI Staff will be at our Exhibit Booth #618:
- Sunday, January 11 – 3:00 PM - 8:30 PM
- Monday, January 12 – 9:30 AM - 5:00 PM
- Tuesday, January 13 – 9:30 AM - 3:00 PM
Saturday, January 10
Sequence Viewer and Genome Workbench - Sequence Display and Analysis Tool
Kim D. Pruitt
Computer Demos 1 C04: 2:30 PM – 2:50 PM, Room: California
The National Center for Biotechnology Information (NCBI) has developed two companion tools to display and analyze sequence and alignment data. Sequence Viewer is an online graphical display tool that offers configurable options for displaying NCBI as well as imported BLAST or local data. This online tool includes options to add and configure display tracks, zoom and pan the display, add (and name) markers, search, download the displayed sequence, and save a high-resolution print friendly PDF file that can be edited in popular image editing tools for figure preparation.... [Full abstract] [Slides-PDF]
Sunday, January 11
Equine Genome Resources at National Center for Biotechnology Information
Shashikant Pujar
Equine 2 Workshop W273: 8:00 AM – 8:15 AM, Room: Royal Palm Salon 5-6
NCBI's Eukaryotic Genome Annotation generates comprehensive sets of genes, transcripts and proteins for finished and unfinished public genome assemblies of a wide range of taxa among invertebrates, vertebrates and plants. Currently, two equine genome annotations (E. caballus and E. przewalskii) are represented in NCBI’s genome resources. Both these genomes incorporate improved features of the annotation pipeline, including the use of RNA-seq data for transcript model prediction. The annotations provide content to other NCBI resources such as Nucleotide, Protein, Blast, Gene and Map Viewer....[Full abstract] [Slides-PDF]
Monday, January 12
Posters: 10:00 AM – 11:30 AM, Room: Exhibit Hall
Improving the Flow of Data to NCBI Sequence Repositories, SRA and GenBank
Ilene Mizrachi
P1112 [Abstract] [Poster-PDF]
National Center for Biotechnology Information Resources for Plant Genomics
Brian Smith-White
P1120 [Abstract] [Poster-PDF]
Sequence Viewer and Genome Workbench - Sequence Display and Analysis Tools for Eukaryotes and Prokaryotes
Kim D. Pruitt
P1142 [Abstract] [Poster-PDF]
Monday, January 12
NCBI Genome Resources Workshop
Moderators/Organizers: Kim D. Pruitt and Tatiana Tatusova
12:50 pm - 3:00 pm, Room: Sunset - Meeting House
This workshop provides an overview of several NCBI genome resources, updates to the NCBI Eukaryotic Genome Annotation pipeline, an annual report on the amount of genome sequencing data available, and information on how to access genomes and their annotation.
Improving the Flow of Data to National Center of Biotechnology Information Sequence Repositories, SRA and Genbank - All Organisms
Ilene Mizrachi
12:50 PM – 1:15 PM
NCBI hosts repositories like SRA and GenBank for the archiving of DNA and RNA sequence data, annotations and associated metadata. These repositories have experienced significant growth in data deposition over the past few years. A Submission Portal (http://submit.ncbi.nlm.nih.gov) is being developed to streamline the submission of sequence data and facilitate deposition of rich descriptive information about the biological sample and experimental metadata. Researchers can submit both the raw sequence reads for both genomic and RNA-Seq studies to SRA (Sequence Read Archive), as well as the assemblies that are derived from these reads to the WGS (Whole Genome Shotgun) and TSA (Transcriptome Shotgun Assembly} resources. There are programmatic and interactive web interfaces to the portal for both the informatics-rich genome center and the individual scientists....[Full abstract] [Slides-PDF]
Variation at NCBI: Resources, Tools and Submissions
Jennifer Lee
1:15 PM – 1:40 PM
We will be summarizing the status of NCBI variation resources and tools, including the Variation resources, Variation Reporter, Variation Viewer, Remap Service and Variation Submission....[Full abstract] [Slides-PDF]
Update on the Eukaryotic Genome Annotation Pipeline
Francoise Thibaud-Nissen
1:40 PM – 2:05 PM
The NCBI Eukaryotic Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/genome/annotation_euk/) provides content for various NCBI resources including RefSeq sequence databases, Gene, BLAST databases and the Map Viewer genome browser. As of November 1st, 2014 the pipeline has been used to annotate over 180 organisms, 100 of them with the help of RNA-Seq data. The pipeline uses a modular framework for the automated execution of all annotation tasks. Core components of the pipeline are the Splign and ProSplign alignment programs and Gnomon, an alignment- and HMM-based gene prediction program, developed at NCBI.....[Full abstract] [Slides-PDF]
From Genes to Genomes – New Features and Data Access
Kim D. Pruitt
2:05 PM – 2:30 PM
The National Center for Biotechnology Information (NCBI) provides several resources to facilitate access to genomes and their annotations. These resources provide a stable identifier and meta-data for assembled genomes (Assembly), a portal to browse available genome-scale data (Genome), gene-specific report pages that include an interactive genome browser (Gene), and comprehensive access to genomes and annotation data via file transfer protocol (FTP). This presentation will highlight recent changes to these resources including updates to NCBI’s Gene resource and will include examples illustrating how to access new information content. [Full abstract] [Slides-PDF]
Annual Report on the Eukaryotic Genome Annotation
Tatiana Tatusova
2:30 PM – 3:00 PM
This presentation will provide an overview on the current number, status, and data availability for eukaryotic genome sequencing projects. [Online abstract] [Slides-PDF]
Monday, January 12
Posters: 3:00 PM – 4:30 PM, Room: Exhibit Hall
New Developments in the NCBI Eukaryotic Genome Annotation Pipeline
Francoise Thibaud-Nissen
P0051 [Abstract] [Poster-PDF]
Genomic Resources for Arabidopsis Research at NCBI
Anjana Raina Vatsan
P0791 [Abstract] [Poster-PDF]
From Genes to Genomes – New Features and Data Access
Kim D. Pruitt
P1105 [Abstract] [Poster-PDF]
dbSNP and dbVar: NCBI Databases of Simple and Structural Variations
Lon Phan
P1109 [Abstract] [Poster-PDF]
Annotation of Laurasiatheria Genomes By National Center for Biotechnology Information (NCBI)
Shashikant Pujar
P1115 [Abstract] [Poster-PDF]
Tuesday, January 13
National Center for Biotechnology Information Resources for Plant Genomic
Brian Smith-White
Computer Demos 3 C214: 12:00 PM – 12:15 PM, Room: California
Plant genomics is a simple expansion of the scope of genomics at the National Center for Biotechnology Information (NCBI). NCBI provides the tools for storage of and analysis of nucleotide sequence such as, respectively, GenBank and BLAST and the capability to provide evidence-based annotation of RefSeq genome sequence. In addition, genomics at NCBI includes NCBI-curated resources such as 1) RefSeq, 2) Entrez Probes, and 3) Entrez Gene, as well as databases and services....[Full abstract] [Slides-PDF]