DNA Databanks - PowerPoint PPT Presentation

DNA Databanks

Speaker: Yu-Chung Chang 張猷忠

Institute of Biochemistry

National Yang-Ming University

GenBank, DDBJ, EMBL,…

Protein databases

PIR, Swiss-Prot, PRF, GenPept, TrEMBL, PDB,…

EST databases

dbEST, DOTS, UniGene, GIs, STACK,…

Structure databases

MMDB, PDB, Swiss-3DIMAGE,…

Pathway databases

KEGG, BRITE, TRANSPATH,…

Integrated databases

SRS

Motif or cis-element databases

Prosite, Pfam, BLOCKS, TransFac, PRINTS, URLs,…

Gene, protein & disease databases

GeneCards, OMIM, OMIA,…

Taxonomy databases

Literature databases

PubMed, Medline,…

Patent database

Apipa, CA-STN, IPN, USPTO, EPO, Beilstein,…

Others…

RNA databases,…

• cDNA resources
• Genbank (NCBI), Nucleotide Sequence Database (EMBL), DDBJ , MGC,…
• Genomic DNA resources
• HTG, dbGSS, GOLD, ERGO,…
• EST resources
• dbEST, UniGene, GIs, STACKS, DOTS,…
• Others
• dbSTS, UniSTS, dbSNP, TransFac, ISIS, Repbase, ...

• GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
• There are approximately 11,720,000,000 bases in 10,897,000 sequence records as of February 2001.
• GenBank is part of the International Nucleotide Sequence Database Collaboration, which is comprised of the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
• http://www.ncbi.nlm.nih.gov/Entrez/

• The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing  projects and patent applications.
• http://www.ebi.ac.uk/Databases/index.html

• Database Search
• Getentry, SFgate & WAIS, SRS, Homology Search, TXSearch, SQmatch
• Data Analysis
• malign, clustal w
• Genome Analysis
• GTOP
• Protein Structure
• PDB Retriever, SSThread, LIBRA I

• Whole genome sequences
• EST projects
• MGC projects
• SNP projects
• GSS projects
• STS projects

Graphs created on 12 Dec 2000

Graphs created on 12 Dec 2000

At this time the following types of submissions are NOT acceptable.

• sequences of less than 50 bp in length.
• computer generated or otherwise predicted sequences (i.e. EST assembled sequences).
• third party sequences downloaded from a sequence database or journal.
• one genomic sequence with multiple exons joined together without the sequence of the intervening introns.
• primer only sequences.

At this time the following types of submissions are NOT acceptable.

• protein only sequences.
• non-biologically contiguous sequences containing internal unsequenced spacers.
• sequences containing a mix of genomic and mRNA sequence represented as a single sequence
• EST submissions should be submitted through the dbEST system.
• as of 1 January, 2000, Genome Survey Sequences (GSSs) should not be submitted through Bankit; use the dbGSS system.

Bankit

WebIn

Sakura

Sequin

e-mail

Sequin

Diskette

Sequin

dbEST

UniGene

dbGSS

dbSTS

UniSTS

RefSeq

MGC

dbSNP

HTGs

UniVec

dbEST

• dbEST is a database of expressed sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes cDNA sequences from differential display experiments and RACE experiments.

• Database of genome survey sequences.
• Short, single pass read genomic sequences.
• Exon trapped sequences.
• Cosmid/BAC/YAC ends.
• Alu PCR sequences.
• GSS sequences are available from two sources: dbGSS and the GSS division of GenBank. The sequences and accession numbers in both sources are the same but the record formats differ.

• Database of sequence tagged sites.
• Short sequences that are operationally unique in the genome, used to generate mapping reagents.
• STS sequences are available from two sources: dbSTS and the STS division of GenBank. The sequences and accession numbers in both sources are the same but the record formats differ.

• High throughput genome sequences from large scale genome sequencing centers.
• Unfinished (phase 0, 1, 2) and finished (phase 3) sequences.
• Sequence data in this division are available for BLAST homology searches against either the "htgs" database or the "month" database, which includes all new submissions for the prior month.

• Database of single nucleotide polymorphisms.
• Small-scale insertions/deletions.
• Polymorphic repetitive elements.
• Microsatellite variation.

• At the May 2000 collaborative meeting DDBJ/EMBL/GenBank agreed to create a new database division HTC to represent unfinished High Throughput cDNA sequences. HTC sequences may include 5'UTR and 3'UTR regions and (part of a) coding region. Upon finishing of these sequences, they will be moved to the corresponding taxonomic division. HTC sequence entries will include the keyword 'HTC'. The keyword will be removed once the entry has been included in the taxonomic division.

• The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources.

• Subject searching
• Phrase searching
• Searching for authors
• Searching for unique identifiers
• Searching by molecular weight
• Range searching
• Truncating searching (Wildcard searching)
• Combining sets

• Text searching
• hiv-1
• Subject terms are automatically combined
• hiv-1 protease, hiv-1 AND protease

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• “hiv-1 protease”
• Using quotes forces Entrez to check a phrase list against which the search terms are matshed.
• It is not adjacency searching.
• If the search phrase is not in the phrase list, Entrez treats it as a subject searching.

• Chang YC
• Search only the author field
• Chang
• Search all fields
• Subject searching
• Do not use punctuation.

• Accession numbers
• GenBank/EMBL/DDBJ: U12345, AF123456
• GenPept: AAA12345
• SwissProt & PIR: P12345
• RefSeq: NM_123456, NT_123456, NP_123456, NC_123456, XM_123456, XP_123456
• Sequence identification numbers
• GI numbers: 6995995
• Version numbers: AF123456.3

• 010600[Molecular Weight]
• 012345[MOLWT]
• 010000:050000[MOLWT]
• 002000:010000[MOLWT] AND human[Organism]
• [field name]  feature table

• Accession numbers [ACCN], sequence length [SLEN], and molecular weight [MOLWT]
• AF114696:AF114714[ACCN]
• Not for GI and Version numbers
• 3000:4000[SLEN]
• 002002:002100[MOLWT]

• Wildcard searching
• Root word plus *
• bacte*, retroviru*
• Only retrieve the first 150 variations of truncated terms
• Left-handed trunction is not possible
• *ology

• Use your search History to combine documents
• #1 AND #4

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• AND, OR, NOT
• bacteria AND virus NOT phage
• (bacteria AND virus) NOT phage
• hiv-1 OR bacterial protease
• hiv OR (bacterial AND protease)

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• You are only intrested in nucleotide sequences from the mouse
• Select Nucleotide database from the black menu bar or the Search pull-down menu.
• Select limits.
• In the "Limits To:" section, select Organism from the Search Field pull-down menu.
• Type "mouse" without quotes in the query box and select Go.

• You are only interested in protein sequences that are less than 50 amino acids in length.
• Select the Protein database from the black menu bar or the Search pull-down menu.
• Select Limits.
• In the "Limited To:" section, select Sequence Length from the Search Field pull-down menu.
• Type "0:50" without quotes in the query box and select Go.

• You are interested in mitochondrial carriers but you do not want the EST sequences.
• Select the Nucleotide database from the black menu bar or the Search pull-down menu.
• Type "mitochondrial carrier" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, checkthe box next to “Exclude ESTs" and select Go.

• You are only interested in Cryptosporidium ribosomal RNA sequences.
• Select the Nucleotide database from the black menu bar or the Search pull-down menu.
• Type "cryptosporidium" without quotes in the query box.
• Select Limits.
• In the "limited to:" section, select the "Molecule" pull-down menu and choose rRNA and select Go.

• You are interested in the genes in the chloroplast of flowering plants.
• Select the Nucleotide database from the black menu bar or the Search pull-down menu.
• Type "flowering plants" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, select the "Gene Location" pull down menu and choose chloroplast and select Go.

• You are interested only in cysteine phosphatase protein sequences submitted directly to PIR.
• Select the Protein database from the black menu bar or the Search pull-down menu.
• Type "cysteine phosphatase" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, select the "Only From" pull-down menu and choose PIR and select Go.

• You want to see any nucleotide sequences from pigs added to the database (or updated) in the last 30 days.
• Select the Nucleotide database from the black menu bar or the Search pull-down menu.
• Type "pigs" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, select Organism from the Search Field pull-down menu.
• And in the "Limited To:" section, select the "Modification Date" pull down menu and choose 30 days and select Go.

• You want to retrieve all mouse or human nucleotide sequences added to the database (or updated) during 1997.
• Select the Nucleotide database from the black menu bar or the Search pull-down menu.
• Type "mouseOR human" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, select Organism from the Search Field pull-down menu.
• And in the "Limited To:" section, select the "Modification Date" pull down menu and choose Modification Date. In the date boxes, type the dates in the format YYYY/MM/DD. You can tab from box to box in the date fields. Select Go.

• You are interested in the protein translations of human GenBank nucleotide sequences added to the protein database (or updated) in the last 30 days. You do not want patent records.
• Select the Protein database from the black menu bar or the Search pull-down menu.
• Type "human" without quotes in the query box.
• Select Limits.
• In the "Limited To:" section, select Organism from the Search Field pull-down menu.
• On the same screen, select the exclude patents check box, select GenBank from the Only From pull-down menu, and finally select 30 days from the Modification Date pull-down menu and select Go.

• Find all human nucleotide sequences with LTR annotations.
• In the Nucleotide database use the following expression -

LTR[FKEY] AND human[ORGN]

• Find drosophila population studies published in the Journal of Molecular Evolution
• In the PopSet database use the following expression -

j mol evol[JOUR] AND drosophila[ORGN]

• Find all human protein sequences with lengths between 50 and 60 amino acids and that were entered into the database during 1999.
• In the Protein database use the following expression -

human[ORGN] AND 50[SLEN]:60[SLEN] AND 1999[MDAT]

Feature key or descriptor line

Feature qualifiers

attenuator

CAAT_signal

CDS

enhancer

exon

gene

GC_signal

iDNA

intron

J_region

LTR

misc_binding

misc_feature

mRNA

polyA_signal

polyA_site

STS

3’UTR

5’clip

ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt

/bound_moiety

/citation

/codon

/codon_start

/cons_splice

/db_xref

/direction

/EC_number

/evidence

/function

/gene

/map

/note

/organism

/phenotype

/rpt_family

/translation

• Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world.

• The purpose of this database is to provide the scientific community with a resource to
• store DNA methylation data
• search for methylation patterns and profiles
• correlate methylation and expression data of genes

• Gene expression is often regulated at the level of mRNA translation. The structural characteristics of mRNA correlate with translation efficiency and specificity. Determination of "active elements" could be very useful for prediction of the gene expression pattern under both normal and stress conditions because not all mRNAs can be translated when stressed. Prediction of the gene expression pattern can might be useful for biotechnology and cDNA analysis.

• RAD (RNA Abundance Database) is a public gene expression database designed to hold data from array-based (microarrays, high-density oligo arrays, macroarrays) and nonarray-based (SAGE) experiments.
• The ultimate goal is to allow comparative analysis of experiments performed by different laboratories using different platforms and investigating different biological systems.

Markets

Restaurents

Cooking skills

Sequencing centers

Nucleotide databases

Value-added databases

Bioinformatics

• Please try to write a search statement for finding all mouse nucleotide sequences with CDS annotations.