# Presentation: 408858

- Kim D. Pruitt
- Transcriptome 2002

- National Center for Biotechnology Information (NCBI)
- National Library of Medicine
- National Institutes of Health
- http://www.ncbi.nlm.nih.gov/

**Notes:**
Title

## Fundamental resources 

**Primary Databases - ****GenBank, dbEST, dbSTS, PubMed**
- Archival - original data submissions
- Database staff organize, but don’t add additional information
**Derivative Databases – ****RefSeq, LocusLink, UniGene, Map Viewer**
- Curated/expert review
- compilation and correction of data
- Computationally Derived
- Combinations

**Notes:**
Fundamental Resources – Primary vs. Derivative databases

## Infrastructure

- BLAST
- Entrez
- Displays
- Navigation – extensive crosslinking

**Integrating Information**
**To Facilitate Discovery, Retrieval,**
**& Navigation**

**Sequences**

**Publications**

**Structure**

**Phenotypes**

**Expression**

**Maps**

**Comparative**
**Genomics**

**Notes:**
Infrastructure

## Increasing Discovery Space

## NCBI Reference Sequences (RefSeq)

- A sequence for each macromolecule of Central Dogma
- Linked on a residue by residue basis
- Objectively non-redundant and comprehensive
**Curated Resource**
- Authoritative source by genome
- Derivative of GenBank but corrected, merged, extended
- Publicly distributed
**Reagents for Genome Annotation and Analysis**
**Substrate for Functional Genomics**

**NCBI Reference Sequences (RefSeq)**

## The Basic Model

## RefSeq: Scope

- The NCBI Reference Sequence (RefSeq) project provides non-redundant sequence data including bacterial and viral genomes, mitochondrion, chromosomes, constructed genomic contigs, transcripts, and  proteins.

**RefSeq: Scope**

**RefSeq as a protein database**
**over 280,000 proteins**

## RefSeq: Products

- Goal: One sequence entry for each naturally occurring molecule

**Key:**
**curated**
**calculated**

- Multiple products for one gene are instantiated as separate RefSeqs with the same LocusID.

## Process Flow

**Process Flow**

**New Genes & Descriptions**
- In-house
- Collaboration

**LocusLink**

**RefSeq**

- BLAST
- Analysis

- Provisional & Predicted Records
-    (Transcripts & Proteins)

- Status

- Reviewed Records
-   (Genomic Regions,Transcripts,
-    Proteins)

**Public Release:**
- LocusLink Web Site

**Accessible in:**
- BLAST
- BLink
- Entrez
- FTP
- LocusLink

**Curation**

- Updates

**BLAST**

**Genome**
**Annotation**
**Pipeline**

**Database support, automated steps, manual curation**

## RefSeq: Curation

**Review**

**Sequence **
**Editing**

**Final Check**

**Public**

**Known Genes**
**Gene Families**
**Gene Clusters**
**Identified Problems**

**Sequence **
**Database data  **
**Literature**

**Correct errors**
**Extend UTRs**
**Splice Variants**
**Annotate Features**

**Quality Control**

**Assignment**

**Simple cases:**
** ****1-2 days**
**Large gene families:**
**months**

**Time**

**Reviewed Records:**
**Human - 4,685 accessions (3,445 genes)**
**Fly – 1,423 accessions (from FlyBase)**
**Mouse,Rat – 45 accessions**

## New Type of RefSeq: Genomic Regions

**Correct Assembly through Duplications, Paralogous Gene Clusters**

**Optimize Annotation in Gene Clusters**

**Why?**

**Used in Genome Annotation Process**

## Maintenance

**New Genes: **
**	****GenBank**
**	****UniGene**
**	****Genome Annotation **
**	****Collaboration**
**	****e-mail**

**Updates:**** **
**	****GenBank updates**
**	****Collaboration**
**	****Ongoing curation**
**	****Genome Annotation**
**	****e-mail**

**Why Look For RefSeqs?**
**Enhanced Discovery Space:**** **
**	****What do we already known?**
**	****Predicted RefSeqs – where do we need to know more?**
**	****Genome Annotation Products (Model RefSeqs)**
**Analysis:**
**	****transcript, protein, annotation, gene index**

**We welcome feedback, suggestions, collaborations**

## Increasing Discovery Space

## LocusLink

**LocusLink**

**Scope:**
**Human**
**Mouse**
**Rat**
**Fly**
**Zebrafish**
**HIV-1**

## LocusLink: Maintenance

**Data Collection:**
**Extensive Collaborations with authoritative groups**
**In-house computation**
**In-house curation effort (RefSeq review)**

## LocusLink: Discovery

- Find novel uncharacterized genes on a finished chromosome
- QUERY= 21[chr] NOT has_omim AND has_homol AND type_gene_protein
- AND predicted
- AND model
- AND provisional
- AND C21orf* OR MGC*

## Increasing Discovery Space

## Map Viewer

- What?
- Genome Assembly
- Genome Annotation
- Integrated map data (genetic, cytogenetic, RH)
- Scope?
- Human
- Drosophila
- Mouse
- (model genomes)
- Why?
- Facilitate discovery (genes, variation ...)
- Facilitate navigation
- Facilitate use of genomic sequence information

## Genome Build Process

**Assembly**

- Input Data:
-   Sequences
-   Curated NTs
-   TPF
-   BLAST hits

- Resource
- Updates

- STS

- Clones

**Annotation**

- RefSeq

**FTP**
**BLAST**
**Input Resources**

**Map Viewer**

**Update:**
- Links
- gi’s

**Sequences (contig mRNA protein)**

**Analysis & Review**
**Corrections for next build**

- LocusLink

- GenBank

- GenomeScan

- dbSNP

**Public Release**

- Exclude
- problem
- accessions

## RefSeq: a reagent for Annotation

**RefSeq: a reagent for Annotation**

**GenomeScan**

**ESTs**

**TBLASTN**

**RPSBLAST**

**RefSeq mRNAs**

**GenBank mRNAs**

- RefSeq Advantages:
- Separate Gene Families
- Not Partial
- Means to correct
-   problem sequences

- Quality Control:
- RefSeq review results
- in excluding problem
- GenBank sequences
- from annotation pipeline

- Potential Problems:
- Gene Families
- Partial sequences
- Chimeric
- Intron read-through
- Linker
- Vector
- Wrong organism

- genome

## What questions can be asked?

- What genes (markers, SNPs) are between 2 markers?
- What BAC clones are available on Xq28?
- Where are there serine kinases?
-  I’ve cloned gene xyz in my favorite organism.  What is related in human?
- What is the evidence that there is a gene at position n?
- I have found a phenotype of interest between markers x and y; what is known about this region?

## Fanconi Syndrome Genetic Mapping

**Pathology in proximal renal tubular transport**

## Query Map Viewer

**Look for genes in the region**

**Psr2p – sodium stress response in yeast**

## BLAST Queries: genomic distribution of matches

**Result from a BLAST query of**
** ****a zinc finger protein**

**Best match**

## Review the alignment

**A click away:**
- Alignments (BLAST hit)
- Gene Description
- Report of all features in the region
- Sequence in the region
- other mRNAs aligning in the region
- Homology Maps
- Model Maker - Define your own gene model based on alignments in the region

##  Homology Maps

**Genes in regions of conserved synteny**

## Map Viewer: Model Maker

## Increasing Discovery Space

## Acknowledgments

**Acknowledgments**

- RefSeq Curator Staff
- BLAST Team
- Entrez Team
- NCBI Service Desk Staff
**Collaborators**:
- Human Gene Nomenclature Committee
- OMIM Staff
- The Jackson Laboratory
- Rat Genome Database

**Genome Build Team:**
- Richa Agarwala
- Hsiu-Chuan Chen
- Slava Chetvernin
- Deanna Church
- Olga Ermolaeva
- Renata Geer
- Wratko Hlavina
- Wonhee Jang
- Jonathan Kans
- Ken Katz
- Paul Kitts
- David Lipman
- Adam Lowe
- Donna Maglott
- Jim Ostell
- Kim Pruitt
- Sergey Resenchuk
- Victor Sapojnikov
- Greg Schuler
- Steve Sherry
- Andrei Shkeda
- Tatiana Tatusova
- Lukas Wagner
- Sarah Wheelan

**http://www.ncbi.nlm.nih.gov/**