Retrieving sequence data from Entrez

NCBI website

ncbi.nlm.nih.gov

NIH

National Institutes of Health

National Institutes of Health (NIH)

one of the 11 operating division of the HHS

HHS

Health & Human Services

National Library of Medicine (NLM)

on of the 27 divisions of the NIH

NLM started by

an army surgeon at 1836

How many databases are found in the NCBI

59

The main database contain ——- databases under ‘All Resources’

39

How many smaller databases are found

20

Gene contains

information about various species links to genome

Nucleotide contains

a source of sequences from different databases

Protein contains

includes protein sequence records from a variety of sources

Protein clusters contains

a collection of related protein sequences, consisting of Ref Seq proteins encoded by complete prokaryotic and organelle plasmids and genomes tool

Genome contains

Contains sequence and map data from the whole genomes of over 1000 organisms. the genomes represent both completely sequenced organisms and those for which sequencing is in progress.

Sequence Length

contains number of nucleotide base pairs in the sequence record

Modification Data

shows the last data of modification

Definition

is a breif descriotion of sequence that includes information such as source organism, gene/protein name, or some description

Accession

number indicates the unique identifier for a sequence record

Organism

Describes the formal scientific name for the source organism and its lineage

Reference

includes publications by the authors of the sequence that discuss the data reported in the record

Type of Data in the Gene bank

collection of all publicly available DNA sequence

Type of Data in the RefSeq

Reference sequences of DNA, RNA, and protein

Features of GeneBank

1. Original submission

2. Any organisms

3. Larger

Features of RefSeq

1. Comprehensive

2. Integrated

3. Non-redundant

4. Well-annotated

5. Better accession number format

RefSeq accession format (NC_)

Genomic (complete genomic molecule)

RefSeq accession format (NG_)

Genomic (Incomplete genomic region)

RefSeq accession format (NM_ , XM_)

mRNA

RefSeq accession format (NR_ , XR_)

RNA

RefSeq accession format (AP_ ,NP_, YP_, XP_, WP_)

Protein