Fundamentals in Sequence     Analysis 1.(part 1)Review of Basic biology + database searching inBiology.              Hugue...
The Flow of Biotechnology         Information Gene                                      Function> DNA sequenceAATTCATGAAAA...
Prequisites to Sequence Analysis• Basic Biology so you can understand the language  of the databases: Central Dogma (trans...
Central Dogmas of Molecular Biology1) The concept of genes is historically defined on the basic of geneticinheritance of a...
Central Dogmas of Molecular Biology3) Each side of the double helix faces it´s complementary base.A T, and G  C.4) Bio...
Central Dogmas of Molecular Biology 6) DNA information is copied over to mRNA that acts as a template to produce proteins....
Prokaryotic genes         Prokaryotes (intronless protein coding genes)Upstream (5’)                            Gene regio...
Why does Nature bothers with the mRNA?Why would the cell want to have an intermediate between DNA andthe proteins it encod...
Prokaryotic genes (operons)      Prokaryotes (operon structure)upstream promoter                                          ...
Bacterial Gene Structure of signals    Bacterial genomes have simple gene structure.    - Transcription factor binding sit...
Genetic CodeHow does an mRNA specify amino acid sequence? The answer lies inthe genetic code. It would be impossible for e...
Codon table              Note the degeneracy of the              genetic code. Each amino acid              might have up ...
RNARNA has the same primary structure as DNA. It consists of a sugar-phosphate  backbone, with nucleotides attached to the...
tRNA ( transfer RNA) is a small RNA that has a very specific secondary and tertiary structure such that it can bind an ami...
Bacterial Gene PredictionMost of the consensus sequences are known from ecolistudies. So for each bacteria the exact distr...
Open Reading FramesThe simplest bacterial gene prediction techniques   simply1) identify all open reading frames(ORFs),2) ...
Open Reading Frames (ORF)On a given piece of DNA, there can be 6 possible frames. The ORF can beeither on the + or minus s...
Eukaryotic Central DogmaIn Eukaryotes ( cells where the DNA is sequestered in a separate nucleus)The DNA does not contain ...
Eukaryotic Nuclear Gene StructureGene prediction for Pol II transcribed genes.• Upstream Enhancer elements.• Upstream Prom...
introns•Transcript region, interrupted by introns. Eachintrons    •starts with a donor site consensus    (G100T100A62A68G8...
Exons•The exons of the transcript region arecomposed of:        •5’UTR (mean length of 769 bp) with a        specific base...
Structure of the Eukaryotic Genome          ~6-12% of human DNA encodes          proteins(higher fraction in          nema...
Non-Coding Eukaryotic DNA    Untranslated regions (UTR’s)    •introns (can be genes within    introns of another gene!)   ...
PseudogenesPseudogenes:        Dna sequence that might code for agene, but that is unable to result in a protein.This defi...
RepeatsEach repeat family has many subfamilies.- ALU: ~ 300nt long; 600,000 elements in humangenome. can cause false homol...
Low-Complexity Elements• When analyzing sequences, one often rely on the  fact that two stretches are similar to infer tha...
Masking•To avoid finding spurious matches in alignment programs, youshould always mask out the query sequence.•Before pred...
More Non-Protein genesrRNA - ribosomal RNA   is one of the structural components of the ribosome. It has sequence   comple...
Protein Processing & localization.The protein as read off from the mRNA may not be in the finalform that will be used in t...
Convention for nucleotides in databaseBecause the mRNA is actually read off the minus strandof the DNA, the nucleotide seq...
Biology Information on the         Internet
Biology Information on the Internet• Introduction to Databases• Searching the Internet for Biology  Information.  – Genera...
• Databases:          – A collection of Records.               – Each record has many fields.  Spread-sheet – Each field c...
gi      Accession version date       Genbank Division taxid organims       Number of Chromosomes6226959 NM_000014       3 ...
gi      Accession version date       Genbank Division taxid organims       Number of Chromosomes6226959 NM_000014       3 ...
Types of Relational databases.• The Internet can be though of as one  enormous relational database.  – The “links”/URL are...
Indexed searches.• To allow easy searching of a database, make  an index.• An index is a list of primary keys  correspondi...
Indexed searches.• Boolean Query: Merging and Intersecting lists:  – AND (in both lists) (e.g. human AND genome)        – ...
Search strategies• Search engines use complex strategies that go  beyond Boolean queries.    – Phrases matching:        • ...
Search strategies• Search engines use complex strategies that  go beyond Boolean queries.• To avoid these term mapping, en...
Indexed searches.Example• find the advanced query page at  http://www.altavista.com• type human (and hit the Search button...
• Search Engines:  – Web Spiders: Collection of All web pages, but    since Web pages change all the time and new    ones ...
• Search Engines:     • www.google.com (BEST!)     • Google ranks pages according to how many pages with those       terms...
• Search Engines:  – Curated Collections: Not comprehensive:    Contains list of best sites for commonly    requested topi...
• Search Engines:  – Meta-Search Engines: Polls several search    engines, and returns the consensus of all results.    Is...
• Virtual Libraries: Curated collections of  links for Biologists.(by Biologists)  – Pedro’s BioMolecular Research Tools:(...
Biological Databases• Nucleotide databases:   – Genbank: International Collaboration      • NCBI(USA), EMBL(Europe), DDBJ ...
• Protein Databases:   – NCBI:   – Swiss Prot:(Free for academic use, otherwise     commercial. Licensing restrictions on ...
• Structure databases:  – PDB: Protein structure database.      • Http://www.rscb.org/pdb/  – MMDB: NCBI’s version of PDB ...
• Litterature databases:  – NCBI: Pubmed: All biomedical litterature.     • Www.ncbi.nlm.nih.gov     • Abstracts and links...
• Database Identifiers: Primary keys  – GI (changes with each sequence update for    NCBI only)       • Annotation may cha...
Primary Databases• A primary Database is a repository of data  derived from experiments or from research  knowledge.  –   ...
Secondary Databases• A secondary database contains information  derived from other sources.  – Refseq (Currated collection...
Genbank Records• A Bank: No attempt at reconciliation.• Submit a sequence  Get an Accession Number!    – Cannot modify se...
Refseq and LocusLink• Attempt to produce 1 mRNA, 1 protein, and  1 genomic gene for each frequently  occuring allele of a ...
Genbank divisionsSequences in genbank are split into various categories based   on1) The quality and type of sequences2) T...
• Genbank Entry type: (and query to restrict to that  field)   – mRNA (1/10000 errors)       • biomol_mRNA [PROP]   – cDNA...
FASTA Format                                        MOST important                                        data format!!!>i...
Modified FASTA Format1) A few tools follow the convention that   lower case sequences are masked. (repeat   masker, some v...
• WIM now will talk about GCG …
Feature table       (NCBI;EMBL/DDBJ)• http://www.ncbi.nlm.nih.gov/collab/FT/index.htm
Genbank Data format    41•   LOCUS     BTA1AT       1380 bp mRNA            MAM       30-APR-1992•   DEFINITION B.taurus m...
Genbank References•   LOCUS     BTA1AT         1380 bp mRNA             MAM       30-APR-1992•   ...•   REFERENCE 1 (bases...
Genbank Source Qualifier•   LOCUS        BTA1AT         1380 bp mRNA     MAM   30-APR-1992•   ...•   FEATURES             ...
Genbank mRNA+CDS features•   mRNA         <1..>1380•   sig_peptide 33..104•     CDS        33..1283•                /codon...
•   ...        Genbank Sequence format•   BASE COUNT       357 a    413 c    322 g    288 t•   ORIGIN•        1 gaccagccct...
EMBL DATA FORMAT• Embl: http://www.ebi.ac.uk/Databases/• http://www.ebi.ac.uk/cgi-bin/emblfetch• Use Accession X63129
DDBJ DATA FORMAT• DDBJ: http://www.ddbj.nig.ac.jp/• http://ftp2.ddbj.nig.ac.jp:8000/getstart-  e.html• Use Accession X6312...
Entrez• Index Based search system. Each field in  the database is searchable individually or as  agregate.  – (e.g. CDS [F...
Entrez• Available neighbours (related documents or  related sequences)• In Pubmed searches: Term mapping to  neighbouring ...
Entrez• http://www.ncbi.nlm.nih.gov/Entrez/• Tutorials:• http://www.ncbi.nlm.nih.gov/Class/MLACo  urse/Genetics/index.html...
SWISSPROT            http://www.expasy.ch/sprot/sprot_details.html1. Core data: protein sequence data; the citation inform...
SWISSPROThttp://www.expasy.ch/cgi-bin/get-random-entry.pl?S
REBASE (Restriction enzymes dataBASE)Restriction enzymes have a pattern recognition sequence, and then    within or a few ...
Exercises•You can work in teams for this.•1a) Use the first 6000 bases of your genomic piece [ or find abacterial genomic ...
Upcoming SlideShare
Loading in …5
×

Central dogma

1,228 views

Published on

Published in: Education
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
1,228
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
17
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Central dogma

  1. 1. Fundamentals in Sequence Analysis 1.(part 1)Review of Basic biology + database searching inBiology. Hugues Sicotte NCBI
  2. 2. The Flow of Biotechnology Information Gene Function> DNA sequenceAATTCATGAAAATCGTATACTGGTCTGGTACCGGCAACACTGAGAAAATGGCAGAGCTCATCGCTAAAGGTATCATCGAATCTGGTAAAGACGTCAACACCATCAACGTGTCTGACGTTAACATCGATGAACTGCTGAACGAAGATATCCTGATCCTGGGTTGCTCTGCCATGGGCGATGAAGTTCTCGAGGAAAGCGAA > Protein sequenceTTTGAACCGTTCATCGAAGAGATCTCTACCAAAATCTCTG MKIVYWSGTGNTEKMAELIAKGIIESGKDVNTINVSDVNIGTAAGAAGGTTGCGCTGTTCGGTTCTTACGGTTGGGGCGA DELLNEDILILGCSAMGDEVLEESEFEPFIEEISTKISGKCGGTAAGTGGATGCGTGACTTCGAAGAACGTATGAACGGC KVALFGSYGWGDGKWMRDFEERMNGYGCVVVETPLIVQNETACGGTTGCGTTGTTGTTGAGACCCCGCTGATCGTTCAGA PDEAEQDCIEFGKKIANIACGAGCCGGACGAAGCTGAGCAGGACTGCATCGAATTTGGTAAGAAGATCGCGAACATCTAGTAGA
  3. 3. Prequisites to Sequence Analysis• Basic Biology so you can understand the language of the databases: Central Dogma (transcription; Translation, Prokaryotes, Eukaryotes,CDS, 3 ´UTR, 5´UTR, introns, exons, promoters, operons, codons, start codons, stop codons,snRNA,hnRNA,tRNA, secondary structure, tertiary structure).• Before you can analyze sequences.. You have to understand their structure.. And know about Basic Biological Database Searching
  4. 4. Central Dogmas of Molecular Biology1) The concept of genes is historically defined on the basic of geneticinheritance of a phenotype. (Mendellian Inheritance)2) The DNA an organism encodes the genetic information. It is made up ofa double stranded helix composed of ribose sugars.Adenine(A), Citosine (C), Guanine (G) and Thymine (T).[note that only 4 values nees be encode ACGT.. Which can be done using 2bits.. But to allow redundant letter combinations (like N means any 4nucleotides), one usually resorts to a 4 bit alphabet.]
  5. 5. Central Dogmas of Molecular Biology3) Each side of the double helix faces it´s complementary base.A T, and G  C.4) Biochemical process that read off the DNA always read it from the 5´´side towards the 3´ side. (replication and transcription).5) A gene can be located on either the ´plus strand´ or the minus strand.But rule 4) imposes the orientation of reading .. And rule 3(complementarity) tells us to complement each base E.g.If the sequence on the + strand is ACGTGATCGATGCTA, the – strandmust be read off by reading the complement of this sequence going´backwards´e.g. TAGCATCGATCACGT
  6. 6. Central Dogmas of Molecular Biology 6) DNA information is copied over to mRNA that acts as a template to produce proteins.We often concentrate on protein coding genes, because proteins arethe building blocks of cells and the majority of bio-active molecules.(but let´s not forget the various RNA genes)
  7. 7. Prokaryotic genes Prokaryotes (intronless protein coding genes)Upstream (5’) Gene region promoter Downstream (3’) TAC DNA Transcription (gene is encoded on minus strand .. And the reverse complement is read into mRNA) ATG mRNA 5´ UTR CoDing Sequence (CDS) 3´ UTR ATG Translation: tRNA read off each codons, 3 bases at a time, starting at start codon until it reaches a STOP codon. protein
  8. 8. Why does Nature bothers with the mRNA?Why would the cell want to have an intermediate between DNA andthe proteins it encodes? •Gene information can be amplified by having many copies of an RNA made from one copy of DNA. •Regulation of gene expression can be effected by having specific controls at each element of the pathway between DNA and proteins. The more elements there are in the pathway, the more opportunities there are to control it in different circumstances. •In Eukaryotes, the DNA can then stay pristine and protected, away from the caustic chemistry of the cytoplasm.
  9. 9. Prokaryotic genes (operons) Prokaryotes (operon structure)upstream promoter downstream Gene 1 Gene 2 Gene 3 In prokaryotes, sometimes genes that are part of the same operational pathway are grouped together under a single promoter. They then produce a pre-mRNA which eventually produces 3 separates mRNA´s.
  10. 10. Bacterial Gene Structure of signals Bacterial genomes have simple gene structure. - Transcription factor binding site. - Promoters -35 sequence (T82T84G78A65C54A45) 15-20 bases -10 sequence (T80A95T45A60A50T96) 5-9 bases - Start of transcription : initiation start: Purine90 (sometimes it’s the “A” in CAT) - translation binding site (shine-dalgarno) 10 bp upstream of AUG (AGGAGG) - One or more Open Reading Frame •start-codon (unless sequence is partial) •until next in-frame stop codon on that strand .. Separated by intercistronic sequences. - Termination
  11. 11. Genetic CodeHow does an mRNA specify amino acid sequence? The answer lies inthe genetic code. It would be impossible for each amino acid to bespecified by one nucleotide, because there are only 4 nucleotides and 20amino acids. Similarly, two nucleotide combinations could only specify16 amino acids. The final conclusion is that each amino acid is specifiedby a particular combination of three nucleotides, called a codon:Each 3 nucleotide code for one amino acid.•The first codon is the start codon, and usually coincides with the AminoAcid Methionine. (M which has codon code ‘ATG’)•The last codon is the stop codon and does NOT code for an amino acid.It is sometimes represented by ‘*’ to indicate the ‘STOP’ codon.•A coding region (abbreviation CDS) starts at the START codon andends at the STOP codon.
  12. 12. Codon table Note the degeneracy of the genetic code. Each amino acid might have up to six codons that specify it. • Different organisms have different frequencies of codon usage. •A handful of species vary from the codon association described above, and use different codons fo different amino acids. How do tRNAs recognize to which codon to bring an amino acid? The tRNA has an anticodon on its mRNA-binding end that is complementary to the codon on the mRNA. Each tRNA only binds the appropriate amino acid for its anticodon.
  13. 13. RNARNA has the same primary structure as DNA. It consists of a sugar-phosphate backbone, with nucleotides attached to the 1 carbon of the sugar. The differences between DNA and RNA are that: 1. RNA has a hydroxyl group on the 2 carbon of the sugar (thus, the difference between deoxyribonucleic acid and ribonucleic acid. 2. Instead of using the nucleotide thymine, RNA uses another nucleotide called uracil: 3. Because of the extra hydroxyl group on the sugar, RNA is too bulky to form a stable double helix. RNA exists as a single-stranded molecule. However, regions of double helix can form where there is some base pair complementation (U and A , G and C), resulting in hairpin loops. The RNA molecule with its hairpin loops is said to have a secondary structure. 4. Because the RNA molecule is not restricted to a rigid double helix, it can form many different stable three-dimensional tertiary structures.
  14. 14. tRNA ( transfer RNA) is a small RNA that has a very specific secondary and tertiary structure such that it can bind an amino acid at one end, and mRNA at the other end. It acts as an adaptor to carry the amino acid elements of a protein to the appropriate place as coded for by the mRNA. T Three- dimensional TertiarySecondary structure of tRNA structure
  15. 15. Bacterial Gene PredictionMost of the consensus sequences are known from ecolistudies. So for each bacteria the exact distribution ofconsensus will change.Most modern gene prediction programs need to be“trained”. E.g. they find their own consensus and assemblyrules given a few examples genes.A few programs find their own rules from a completelyunannotated bacterial genome by trying to find conservedpatterns. This is feasible because ORF’s restrict thesearch space of possible gene candidates.E.g. selfid program(selfid@igs.cnrs-mrs.fr)
  16. 16. Open Reading FramesThe simplest bacterial gene prediction techniques simply1) identify all open reading frames(ORFs),2) and blastx them against known proteins.3) The ORFs with the best homology are retained first.4) This usually densely covers the bacterial genomes with genes. rRNA and tRNA are detected separately using tRNAScan or blastn.
  17. 17. Open Reading Frames (ORF)On a given piece of DNA, there can be 6 possible frames. The ORF can beeither on the + or minus strand and on any of 3 possible framesFrame 1: 1st base of start codon can either start at base 1,4,7,10,...Frame 2: 1st base of start codon can either start at base 2,5,8,11,...Frame 3: 1st base of start codon can either start at base 3,6,9,12,...(frame –1,-2,-3 are on minus strand)Some programs have other conventions for naming frames.. (0..5, 1-6, etc)Gene finding ineukaryotic cDNA usesORF finding +blastx aswell.http://www.ncbi.nlm.nih.gov/gorf/gorf.htmltry with gi=41 ( or yourown piece of DNA)
  18. 18. Eukaryotic Central DogmaIn Eukaryotes ( cells where the DNA is sequestered in a separate nucleus)The DNA does not contain a duplicate of the coding gene, rather exons must be spliced.( many eukaryotes genes contain no introns! .. Particularly true in ´lower´ organisms)mRNA – (messenger RNA) Contains the assembled copy of the gene. The mRNA acts as amessenger to carry the information stored in the DNA in the nucleus to the cytoplasmwhere the ribosomes can make it into protein.
  19. 19. Eukaryotic Nuclear Gene StructureGene prediction for Pol II transcribed genes.• Upstream Enhancer elements.• Upstream Promoter elements.• GC box(-90nt) (20bp), CAAT box(-75 nt)(22bp)• TATA promoter (-30 nt) (70%, 15 ntconsensus (Bucher et al (1990))• 14-20 nt spacer DNA• CAP site (8 bp)• Transcription Initiation.• Transcript region, interrupted by introns.Translation Initiation (Kozak signal 12 bpconsensus) 6 bp prior to initiation codon.• polyA signal (AATAAA 99%,other)
  20. 20. introns•Transcript region, interrupted by introns. Eachintrons •starts with a donor site consensus (G100T100A62A68G84T63..) •Has a branch site near 3’ end of intron (one not very conserved consensus UACUAAC) •ends with an acceptor site consensus. (12Py..NC65A100G100) UACUAAC AG
  21. 21. Exons•The exons of the transcript region arecomposed of: •5’UTR (mean length of 769 bp) with a specific base composition, that depends on local G+C content of genome) •AUG (or other start codon) •Remainder of coding region •Stop Codon •3’ UTR (mean length of 457, with a specific base composition that depends on local G+C content of genome)
  22. 22. Structure of the Eukaryotic Genome ~6-12% of human DNA encodes proteins(higher fraction in nematode) ~10% of human DNA codes for UTR ~90% of human DNA is non- coding.
  23. 23. Non-Coding Eukaryotic DNA Untranslated regions (UTR’s) •introns (can be genes within introns of another gene!) •intergenic regions. - repetitive elements - pseudogenes (dead genes that may(or not) have been retroposed back in the genome as a single-exon “gene”
  24. 24. PseudogenesPseudogenes: Dna sequence that might code for agene, but that is unable to result in a protein.This deficiency might be in transcription (lack ofpromoter, for example) or in translation or both.Processed pseudogenes: Gene retroposed back in the genomeafter being processed by the splicing apperatus.Thus it is fully spliced and has polyA tail.Insertion process flanks mRNA sequence withshort direct repeats.Thus no promoters.. Unless is accidentallyretroposed downstream of the promotersequence.Do not confuse with single-exon genes.
  25. 25. RepeatsEach repeat family has many subfamilies.- ALU: ~ 300nt long; 600,000 elements in humangenome. can cause false homology with mRNA.Many have an Alu1 restriction site.- Retroposons. ( can get copied back intogenome) - Telltale sign: Direct or inverted repeat flank the repeated element. That repeat was the priming site for the RNA that was inserted.LINEs (Long INtersped Elements) L1 1-7kb long, 50000 copies Have two ORFs!!!!! Will cause problemsfor gene prediction programs.SINEs (Short Intersped Elements)
  26. 26. Low-Complexity Elements• When analyzing sequences, one often rely on the fact that two stretches are similar to infer that they are homologous (and therefore related).. But sequences with repeated patterns will match without there being any philogenetic relation!• Sequences like ATATATACTTATATA which are mostly two letters are called low-complexity.• Triplet repeats (particularly CAG) have a tendency to make the replication machinery stutter.. So they are amplified.• The low-complexity sequence can also be hidden at the translated protein level.
  27. 27. Masking•To avoid finding spurious matches in alignment programs, youshould always mask out the query sequence.•Before predicting genes it is a good idea to mask out repeats (atleast those containing ORFs).•Before running blastn against a genomic record, you must maskout the repeats.•Most used Programs:CENSOR:Repeat Masker:http://ftp.genome.washington.edu/cgi-bin/RepeatMasker
  28. 28. More Non-Protein genesrRNA - ribosomal RNA is one of the structural components of the ribosome. It has sequence complementarity to regions of the mRNA so that the ribosome knows where to bind to an mRNA it needs to make protein from.snRNA - small nuclear RNA is involved in the machinery that processes RNAs as they travel between the nucleus and the cytoplasm.hnRNA – hetero-nuclear RNA. small RNA involved in transcription.
  29. 29. Protein Processing & localization.The protein as read off from the mRNA may not be in the finalform that will be used in the cell. Some proteins contains• Signal Peptide (located at N-terminus (beginning)), this signalpeptide is used to guide the protein out of the nucleus towards it´sfinal cellular localization. This signal peptide is cleaved-out atthe cleavage site once the protein has reach (or is near) it´s finaldestination.•Various Post-Translational modifications (phosphorylation)The final protein is called the “mature peptide”
  30. 30. Convention for nucleotides in databaseBecause the mRNA is actually read off the minus strandof the DNA, the nucleotide sequence are always quotedon the minus strand.In bioinformatics the sequence format does NOT make adifference between Uracil and Thymine. There is nosymbol for Uracil.. It is always represented by a ´T´Even genomic sequence follows that convention. A geneon the ´plus´ strand is quoted so that it is in the samestrand as it´s product mRNA.
  31. 31. Biology Information on the Internet
  32. 32. Biology Information on the Internet• Introduction to Databases• Searching the Internet for Biology Information. – General Search methods – Biology Web sites• Introduction to Genbank file format.• Introduction to Entrez and Pubmed• Ref: Chapters 1,2,5,6 of “Bioinformatics”
  33. 33. • Databases: – A collection of Records. – Each record has many fields. Spread-sheet – Each field contain specific information. Flat-file – Each field has a data type. version of a » E.g. money, currency,Text Field, Integer, date,address(text field) ,citation (text field) database. – Each record has a primary key. A UNIQUE identifier that unambiguously defines this record.gi Accession version date Genbank Division taxid organims Number of Chromosomes6226959 NM_000014 3 06/01/00 PRI 9606 homo sapiens 22 diploid + X+Y6226762 NM_000014 2 10/12/99 PRI 9606 homo sapiens 22 diploid + X+Y4557224 NM_000014 1 02/04/99 PRI 9606 homo sapiens 22 diploid + X+Y 41 X63129 1 06/06/96 MAM 9913 bos taurus 29+X+Y
  34. 34. gi Accession version date Genbank Division taxid organims Number of Chromosomes6226959 NM_000014 3 01/06/2000 PRI 9606 homo sapiens 22 diploid + X+Y6226762 NM_000014 2 12/10/1999 PRI 9606 homo sapiens 22 diploid + X+Y4557224 NM_000014 1 04/02/1999 PRI 9606 homo sapiens 22 diploid + X+Y 41 X63129 1 06/06/1996 MAM 9913 bos taurus 29+X+Y Gi = Genbank Identifier: Unique Key : Primary Key GI Changes with each update of the sequence record. Accession Number: Secondary key: Points to same locus and sequence despite sequence updates. Accession + Version Number equivalent to Gi
  35. 35. gi Accession version date Genbank Division taxid organims Number of Chromosomes6226959 NM_000014 3 01/06/2000 PRI 9606 homo sapiens 22 diploid + X+Y6226762 NM_000014 2 12/10/1999 PRI 9606 homo sapiens 22 diploid + X+Y4557224 NM_000014 1 04/02/1999 PRI 9606 homo sapiens 22 diploid + X+Y 41 X63129 1 06/06/1996 MAM 9913 bos taurus 29+X+YRelational Database (Normalizing a database for repeated sub-elements of a database.. Splitting it into smaller databases, relatingthe sub-databases to the first one using the primary key.) gi Accession version date Genbank Division taxid 6226959 NM_000014 3 01/06/2000 PRI 9606 6226762 NM_000014 2 12/10/1999 PRI 9606 4557224 NM_000014 1 04/02/1999 PRI 9606 41 X63129 1 06/06/1996 MAM 9913 taxid organims Number of Chromosomes 9606 homo sapiens 22 diploid + X+Y 9913 bos taurus 29+X+Y
  36. 36. Types of Relational databases.• The Internet can be though of as one enormous relational database. – The “links”/URL are the primary keys.• SQL (Standard Query Language) – Sybase; Oracle ; Access; (Databases systems) • Sybase used at NCBI. – SRS(One type of database querying system of use in Biology)
  37. 37. Indexed searches.• To allow easy searching of a database, make an index.• An index is a list of primary keys corresponding to a key in a given field (or to a collection of fields) Genbank division PRI 6226959;6226762;4557224;… MAM 41;… Accession NM_000014 6226959;6226762;4557224; X63129 41;
  38. 38. Indexed searches.• Boolean Query: Merging and Intersecting lists: – AND (in both lists) (e.g. human AND genome) – +human +genome – human && genome – OR (in either lists) (e.g. human OR genome) – human || genome
  39. 39. Search strategies• Search engines use complex strategies that go beyond Boolean queries. – Phrases matching: • human genome -> “human genome” – togetherness: documents with human close to genome are scored higher. – Term expansion & synomyms: • human -> homo sapiens – neigbours: – human genome-> genome projects, chromosomes,genetics – Frequency of links (www.google.com)• To avoid these term mapping, enclose your queries in quotes: “human” AND “genome”
  40. 40. Search strategies• Search engines use complex strategies that go beyond Boolean queries.• To avoid these term mapping, enclose your queries in quotes: “human” AND “genome”• To require that ALL the terms in your query be important, precede them with a “+” . This also prevents term mapping.• To force the order of the words to be important, group sentences within strings. “biology of mammals”.
  41. 41. Indexed searches.Example• find the advanced query page at http://www.altavista.com• type human (and hit the Search button)• Type genome:• type human AND genome• type “human genome” (finds the least matches)• type human OR genome (finds the most matches)
  42. 42. • Search Engines: – Web Spiders: Collection of All web pages, but since Web pages change all the time and new ones appear, they must constantly roam the web and re-index.. Or depend on people submitting their own pages. • www.google.com (BEST!) • www.infoseek.com • www.lycos.com • www.exite.com • www.webcrawler.com • www.lycos.com • www.looksmart.com (country specific)
  43. 43. • Search Engines: • www.google.com (BEST!) • Google ranks pages according to how many pages with those terms refer to the pages you are asking for. Not only must one document contain ALL the search terms, but other documents which refer to this one must also contain all the terms. • Great when you know what you are looking for! You can also use “” to require immediate proximity and order of terms. • E.g. type » Web server for the blast program. But google only indexes about 40% of the web.. So you may have to use other web spiders. (disclaimer.. I don’t own stock in that company.. But I’d like to)
  44. 44. • Search Engines: – Curated Collections: Not comprehensive: Contains list of best sites for commonly requested topics, but is missing important sites for more specialized topics (like biology) • www.yahoo.com (Has travel maps too!) – Answer-based curated collections: Easy to use english-like queries. First looks at list of predefined answers, then refines answers based on user interaction. Also answer new questions. • www.askjeeves.com • www.magellan.com • www.altavista.com(has translation TOOLS) • www.hotbot.com
  45. 45. • Search Engines: – Meta-Search Engines: Polls several search engines, and returns the consensus of all results. Is likely to miss sites, but the sites it returns are very relevant to the query. – Other operating mode is to return the sum of all the results.. Then becomes very sensitive to a very detailled query. • www.metacrawler.com • www.savvysearch.com • www.1blink.com (fast) • www.metafind.com • www.dogpile.com
  46. 46. • Virtual Libraries: Curated collections of links for Biologists.(by Biologists) – Pedro’s BioMolecular Research Tools:(1996) • http://www.public.iastate.edu/~pedro/ – Virtual Library: Bio Sciences • http://vlib.org/Biosciences.html – Publications and abstract search. • http://www.ncbi.nlm.nih.gov/ – Expasy server • http://www.expasy.ch – EBI Biocatalog (software & databases list) • http://www.ebi.ac.uk/biocat/
  47. 47. Biological Databases• Nucleotide databases: – Genbank: International Collaboration • NCBI(USA), EMBL(Europe), DDBJ (Japan and Asia) • A “bank” No curation.. Submission to these database is required for publication in a journal. – Organism specific databases (Exercize: Find URLs using search engines) • FlyBase • ChickGBASE • pigbase • wormpep • YPD (Yeast Protein Database) • SGD(Saccharomyces Genome Database)
  48. 48. • Protein Databases: – NCBI: – Swiss Prot:(Free for academic use, otherwise commercial. Licensing restrictions on discoveries made using the DB. 1998 version free of any licensing) • http://www.expasy.ch(latest pay version) • NCBI has the latest free version. • Translated Proteins from Genbank Submissions – EMBL • TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT – PIR
  49. 49. • Structure databases: – PDB: Protein structure database. • Http://www.rscb.org/pdb/ – MMDB: NCBI’s version of PDB with entrez links. • Http://www.ncbi.nlm.nih.gov• Genome Mapping Information: – http://www.il-st-acad-sci.org/health/genebase.html – NCBI(Human) – Genome Centers: • Stanford, Washington University, Stanford – Research Centers and Universities
  50. 50. • Litterature databases: – NCBI: Pubmed: All biomedical litterature. • Www.ncbi.nlm.nih.gov • Abstracts and links to publisher sites for – full text retrieval/ordering – journal browsing. – Publisher web sites. – Biomednet: Commercial site for litterature search.• Pathways Database: – KEGG: Kyoto Encyclopedia of Genes and Genomes: www.genome.ad.jp/kegg/kegg/html
  51. 51. • Database Identifiers: Primary keys – GI (changes with each sequence update for NCBI only) • Annotation may change without the gi changing! – Accession(stable) – version(changes with each sequence update) – “Version” also refers to Accession.version – Secondary accession: Records may have been merged in the past.. So the records which were not chosen as the primary were made secondary.
  52. 52. Primary Databases• A primary Database is a repository of data derived from experiments or from research knowledge. – Genbank (Nucleotide repository) – Protein DB, Swissprot – PDB (MMDB) are primary databases. – Pubmed (litterature) – Genome Mapping databases. – Kegg Database.(pathways)
  53. 53. Secondary Databases• A secondary database contains information derived from other sources. – Refseq (Currated collection of Genbank at NCBI) – Unigene (Clustering of ESTs at NCBI)• Organism-specific databases are often a mix between primary and secondary.
  54. 54. Genbank Records• A Bank: No attempt at reconciliation.• Submit a sequence  Get an Accession Number! – Cannot modify sequences without submitter’s consent. – No attempt at reconciliation.(not a unique collection per LOCUS/gene) – Entries of various sequence quality and different sources==> Separate in various divisions based on • High Quality sequences in taxon specific divisions. • Low Quality sequences in Usage specific databases.• A Collaboration between NCBI, EMBL and DDBJ. They contain (nearly) the same information, only the data format differs.EMBL does not differentiate between the different types of RNArecords, while NCBI (and DDBJ) do. In Entrez EMBL records arepatched up to add that information.
  55. 55. Refseq and LocusLink• Attempt to produce 1 mRNA, 1 protein, and 1 genomic gene for each frequently occuring allele of a protein expressing gene.• www.ncbi.nlm.nih.gov/LocusLink• Special non-genbank Accession numbers – NM_nnnnnn mRNA refseq – NP_nnnnnn protein refseq – NC_nnnnnn refseq genomic contig – NT_nnnnnn temporary genomic contig – NX_nnnnnn predicted gene
  56. 56. Genbank divisionsSequences in genbank are split into various categories based on1) The quality and type of sequences2) The high quality nucleotide sequences are divided into organism-dependant divisions.
  57. 57. • Genbank Entry type: (and query to restrict to that field) – mRNA (1/10000 errors) • biomol_mRNA [PROP] – cDNA (EST, 95-99% accuracy, single pass ) • gbdiv_EST [PROP] – genomic ( biomol_genomic [PROP]) • in HTGS division: >99% accuracy; – gbdiv_HTG [PROP] • GSS(low-quality genome survey sequences) – gbdiv_GSS [PROP] • rest of Genbank; 1/10000 accuracy. – Human gbdiv_PRI [PROP] – mouse gbdiv_ROD [PROP] – bovine gbdiv_MAM [PROP] – STS(EST or cDNA used in mapping) • gbdiv_STS [PROP]
  58. 58. FASTA Format MOST important data format!!!>identifier descriptive textnucleotide of amino-acidsequence on multiple lines if needed.Example:>gi|41|emb|X63129.1|BTA1AT B.taurus mRNA for alpha-1-anti-trypsinGACCAGCCCTGACCTAGGACAGTGAATCGATAATGGCACTCTCCATCACGCGGGGCCTTCTGCTGCTGGC ….
  59. 59. Modified FASTA Format1) A few tools follow the convention that lower case sequences are masked. (repeat masker, some versions of blast, megablast, blastz)2) A few analysis tools (like CLUSTAL) want a simplified identifier on the defline.. So they can have a short string for the alignment.>X63129.1GACCAGCCCTGACCTAGGACAGTGAATCGATAATGGCACTCTCCATCACGCGGGGCCTTCTGCTGCTGGC ….
  60. 60. • WIM now will talk about GCG …
  61. 61. Feature table (NCBI;EMBL/DDBJ)• http://www.ncbi.nlm.nih.gov/collab/FT/index.htm
  62. 62. Genbank Data format 41• LOCUS BTA1AT 1380 bp mRNA MAM 30-APR-1992• DEFINITION B.taurus mRNA for alpha-1-antitrypsin.• ACCESSION X63129• NID g41• VERSION X63129.1 GI:41• KEYWORDS alpha-1 antitrypsin; serine protease inhibitor; serpin.• SOURCE Bos taurus.• ORGANISM Bos taurus• Eukaryota; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria;• Artiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bos.
  63. 63. Genbank References• LOCUS BTA1AT 1380 bp mRNA MAM 30-APR-1992• ...• REFERENCE 1 (bases 1 to 1380)• AUTHORS Sinha,D.• TITLE Direct Submission• JOURNAL Submitted (22-OCT-1991) D. Sinha, Dept of Biochemistry, Temple University, 3400 North Broad Street, Philadelphia, PA 19140, USA• REFERENCE 2 (bases 1 to 1380)• AUTHORS Sinha,D., Bakhshi,M.R. and Kirby,E.P.• TITLE Complete cDNA sequence of bovine alpha 1-antitrypsin• JOURNAL Biochim. Biophys. Acta 1130 (2), 209-212 (1992)• MEDLINE 92223096• FEATURES Location/Qualifiers•
  64. 64. Genbank Source Qualifier• LOCUS BTA1AT 1380 bp mRNA MAM 30-APR-1992• ...• FEATURES Location/Qualifiers• source 1..1380• /organism="Bos taurus"• /db_xref="taxon:9913"• /tissue_type="liver"• /cell_type="hepatocyte"• /clone_lib="lambda gt11"• /clone="2f-Ic"• mRNA <1..>1380• sig_peptide 33..104• ...
  65. 65. Genbank mRNA+CDS features• mRNA <1..>1380• sig_peptide 33..104• CDS 33..1283• /codon_start=1• /product="alpha-1-antitrypsin"• /protein_id="CAA44840.1"• /db_xref="PID:g42"• /db_xref="GI:42"• /db_xref="SWISS-PROT:P34955"• / translation="MALSITRGLLLLAALCCLAPISLAGVLQGHAVQETDDTSHQEAACH KIAPNLANFAFSIYHHLAHQSNTSNIFFSPVSIASAFAMLSLGAKGNTHTEILKGL GFNLTELAEAEIHKGFQHLLHTLNQPNHQLQLTTGNGLFINESAKLVDTFLEDV KNLYHSEAFSINFRDAEEAKKKINDYVEKGSHGKIVELVKVLDPNTVFALVNYI SFKGKWEKPFEMKHTTERDFHVDEQTTVKVPMMNRLGMFDLHYCDKLASWV LLLDYVGNVTACFILPDLGKLQQLEDKLNNELLAKFLEKKYASSANLHLPKLSI SETYDLKSVLGDVGITEVFSDRADLSGITKEQPLKVSKALHKAALTIDEKGTEA VGSTFLEAIPMSLPPDVEFNRPFLCILYDRNTKSPLFVGKVVNPTQA"• mat_peptide 105..1280• /product="alpha-1-antitrypsin"• polyA_signal 1343..1348
  66. 66. • ... Genbank Sequence format• BASE COUNT 357 a 413 c 322 g 288 t• ORIGIN• 1 gaccagccct gacctaggac agtgaatcga taatggcact ctccatcacg cggggccttc• 61 tgctgctggc agccctgtgc tgcctggccc ccatctccct ggctggagtt ctccaaggac• 121 acgctgtcca agagacagat gatacatccc accaggaagc agcgtgccac aagattgccc• 181 ccaacctggc caactttgcc ttcagcatat accaccattt ggctcatcag tccaacacca• 241 gcaacatctt cttctccccc gtgagcatcg cttcagcctt tgcgatgctc tccctgggag• 301 ccaagggcaa cactcacact gagatcctga agggcctggg tttcaacctc actgagctcg• 361 cagaggctga gatccacaaa ggctttcagc atcttctcca caccctgaac cagccaaacc• ...• 1321 gtccccccac tccctccatg gcattaaagg atgactgacc tagccccgaa aaaaaaaaaa• //
  67. 67. EMBL DATA FORMAT• Embl: http://www.ebi.ac.uk/Databases/• http://www.ebi.ac.uk/cgi-bin/emblfetch• Use Accession X63129
  68. 68. DDBJ DATA FORMAT• DDBJ: http://www.ddbj.nig.ac.jp/• http://ftp2.ddbj.nig.ac.jp:8000/getstart- e.html• Use Accession X63129• Flat file format same as NCBI/Genbank format.
  69. 69. Entrez• Index Based search system. Each field in the database is searchable individually or as agregate. – (e.g. CDS [FKEY]) – default is agregate [ALL FIELDS] *• All primary databases are interlinked as one big relational database. – (e.g. Pubmed links in Genbank records)• Phrase matching. – Human genome -> “human genome”
  70. 70. Entrez• Available neighbours (related documents or related sequences)• In Pubmed searches: Term mapping to neighbouring documents and neighbouring terms.• Term mapping to chemical names. – In pubmed: term [All Fields] is term mapped to chemical names + MeSH terms + Text Fields. – .. Unless “term” is whithin double quotes.
  71. 71. Entrez• http://www.ncbi.nlm.nih.gov/Entrez/• Tutorials:• http://www.ncbi.nlm.nih.gov/Class/MLACo urse/Genetics/index.html• http://www.ncbi.nlm.nih.gov/Literature/pubmed_search.• http://www.ncbi.nlm.nih.gov/Database.tut1.html
  72. 72. SWISSPROT http://www.expasy.ch/sprot/sprot_details.html1. Core data: protein sequence data; the citation information and the taxonomic data2. Annotation • Function(s) of the protein • Domains and sites. For example calcium binding regions, ATP- binding sites, zinc fingers, homeobox, kringle, etc. • Post-translational modification(s). For example carbohydrates, phosphorylation, acetylation, GPI-anchor, etc. • Secondary structure • Quaternary structure. For example homodimer, heterotrimer, etc • Similarities to other proteins • Disease(s) associated with deficiencie(s) in the protein • Sequence conflicts, variants, etc.
  73. 73. SWISSPROThttp://www.expasy.ch/cgi-bin/get-random-entry.pl?S
  74. 74. REBASE (Restriction enzymes dataBASE)Restriction enzymes have a pattern recognition sequence, and then within or a few bases away from that pattern is the actual cutting sitehttp://rebase.neb.com/rebase/rebase.htmlI prefer the bairoch format (SWISSPROT format)http://rebase.neb.com/rebase/rebase.f19.htmlID enzyme nameET enzyme typeOS microorganism namePT prototypeRS recognition sequence, cut siteMS methylation site (type)CR commercial sources for the restriction enzymeCM commercial sources for the methylaseRN [count]RA authorsRL jour, vol, pages, year, etc.
  75. 75. Exercises•You can work in teams for this.•1a) Use the first 6000 bases of your genomic piece [ or find abacterial genomic or mRNA sequence in Entrez with length between2000:10000 ]•b) Use the ORF finder to find the gene(s). Compare the answer youget to the annotation you can infer from using blastn against genbankand to using blastx against a protein database.•Do the Entrez exercizes. ( separate word document)

×