Bioinformatics for Genomic and Proteomic data analysis

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Bioinformatics for Genomic and Proteomic data
analysis

• Sequence Analysis

-- Gene Prediction
-- Alignment techniques (BLAST, PSI-BLAST)
-- Major databases and retrieval techniques.
-- Predicting Function, domains etc.
-- finding homology between sequences,
identifying repeats etc (DOTPLOT).
-- Predicting phyico-chemical properties of
protein (ProtParam).
-- Predicting signal peptides and transmembrane
proteins (SignalP).
-- Phylogenetic analysis

• Structure analysis

-- Analysis of Protein structure and conformation
(Rasmol, SwissPDBViewer, VMD etc).
-- Protein structure predictions- Homology
modeling (SwissModel, Modeller).

• Some practical applications

-- Sequence analysis
-- Structure analysis
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Major Bioinformatics databases, Search engines
and data formats.
By Sachin Pundhir Bioinformatics
sub-centre DAVV, Indore
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Database

• Collection of records and files
• Organized for a particular purpose
• Tables
• Tuples (records)
• Attributes
• Values

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BIO520 Student Database

• 1998
• Name ID Grade
• Amy 123 A
• Joe 456 B
• Sue 789 C

.
.
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Database Operations
1998 Name ID Grade Amy 123 A Joe 456
B Sue 789 C

• Tables
• Create, delete
• Tuples (Records)
• Read,write, delete
• Search, sort, modify, print

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International Nucleotide Sequence Database
Collaboration (INSDC)

• Consists of
• DDBJ (Japan)
• GenBank (USA)
• EMBL Nucleotide Sequence Database.
• The three databases exchange new and updated data
  on a daily basis to achieve optimal
  synchronisation.

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Bioinformatics databases

• Protein sequence database
• Genpept Protein sequence database.
• UniProtKB/Swiss-Prot curated protein sequence
  database, minimal level of redundancy and high
  level of integration with other databases.
• UniProtKB/TrEMBL computer-annotated supplement
  of Swiss-Prot that contains all the
  translations of EMBL nucleotide sequence
  entries not yet integrated in Swiss-Prot.
• Refseq Well curated, non-redundant database.

• Nucleotide sequence database
• Genbank Nucleotide sequence database. Highly
  redundant.
• DDBJ DNA Data Bank of Japan.
• EMBL nucleotide sequence database.
• Refseq integrated, non-redundant set of
  sequences, including genomic DNA, transcript
  (RNA), and protein products, for major research
  organisms.

• Structure Database
• PDB Protein Data Bank
• MMDB Molecular Modeling Database

Primary databases
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GenBank Record

• Header
• information that apply to the whole record
• Features
• annotations on the record
• Sequence

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GenBank Record
GeneBank Record
Header
modification date
Molecule Type
Locus Name
Sequence Length
Modification Date
Accession Number
Version Number
GenBank Division
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GeneBank Record
FEATURE
Link to Seq
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GenBank Record
Sequence
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Using Entrez

• An integrated database
• search and retrieval system

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WWWAccess
Entrez BLAST
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Entrez Database Integration
Word weight
PubMed abstracts
3-D Structure
3 -D Structure
Taxonomy
VAST
Genomes
Phylogeny
Protein sequences
Nucleotide sequences
BLAST
BLAST
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The (ever expanding) Entrez System
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Database Searching with Entrez

• Using limits and field restriction to find human
  MutL homolog
• Linking and neighboring with MutL

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Global Entrez Search
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Document SummariesMutLAll Fields
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Entrez Nucleotides Limits Preview/Index
Tabs
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Entrez Nucleotides Limits
Exclude bulk sequences
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Entrez Nucleotides Limits
Title Definition
Exclude Bulk Sequences
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Document Summaries Limits
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Adding Terms Preview/Index
Accession All Fields Author Name EC/RN
Number Feature key Filter Gene Name Issue Journal
Name Keyword Modification Date Organism Page
Number Primary Accession Properties Protein
Name Publication Date SeqID String Sequence
Length Substance Name Text Word Title Uid Volume
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Human MutL Search Results
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Human MutL RefSeq
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NM_000249 Links
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Literature Links

• PubMed
• OMIM

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NM_000249 PubMed
Books
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Books Link
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OMIM Human Disease Genes
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Sequence Links

• Nucleotide Protein

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NM_000249 Related Sequences
similarity
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Taxonomy Link

• The Tax Browser
• NCBIs Taxonomy

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Taxonomy Link
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The Tax Browser
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Batch Downloads
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Batch Downloads FASTA and GI list
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Batch Entrez / Entrez-utilities
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NCBI Protein Databases

• GenPept GenBank, EMBL, DDBJ CDS translations
• RefSeq mRNA based (NP_) and genome based (XP_)
• Swiss-Prot curated high quality protein reviews
• PIR protein information resource Georgetown
  University
• PRF protein resource foundation
• PDB Protein Databank sequences from structures

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Protein Link
BLAST Link
Conserved Domains
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Related Proteins Redundancy
Redundant Sequences
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Related Proteins Links
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BLink non-redundant relatives
Arabidopsis homolog
Conserved Domain
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MLH1 Domain Structure CDD
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MLH1 ATPase Domain
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ATPase structural alignment
ATP Binding site helix
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Genome Resources
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NM_000249 Genome Links
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Higher Genome Resources
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MLH1 UniGene Cluster
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ESTs in UniGene
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The New Homologene

• No longer UniGene based
• Protein similarities first
• Guided by taxonomic tree
• Includes orthologs and paralogs

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The New Homologene
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Entrez Genes integrated gene-based access

• LocusLink
• Complete Genomes
• eukaryotic
• microbial
• organelle

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Genes MLH1 Central Resource
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• QUESTIONS!!!