Functional and structural genomics using PEDANT

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Functional and structural genomics using PEDANT

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Introduction

• With increasing biological sequence data, it need
  a system with ability of storing and retreving
  tens of gigabytes of data, a mature database
  management system, and a good visualization tools

• From case-oriented sequence analysis work to
  automated large-scale genome annotation

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Introduction-PEDANT

• Difference of existing genome analysis programs
• protein oriented vs. DNA oriented analysis
• interactive work vs. commandline operation
• bioinformatics method applied
• user interface
• conveniency feature, project management and data
  editors
• fidelity of result produced
• Benchmark may vary in terms of chosen of balance
  between sensitivity and selectivity of the
  analyses
• PEDANT (Protein Extraction, Description, and
  ANalysis Tool) was available in mid-1997(use
  FASTA as similarity search)
• a workhorse for general bioinformatics research
• a common framework for a number of genome
  analysis projects
• a complete database of automated genomes
• a tool for routine analysis of large amounts of
  genomic contigs and ESTs

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System Architecture

• Overview
• database module storing, modifying and accessing
  data
• processing module bioinformatics computations
• user interface web based communication

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System Architecture-Cont.

• Data access
• primary table store raw data (ex DNA, protein
  sequences and program results ex BLAST output )
• secondary table parsed program results
• simplified schema
• Operation in command line mode
• applying bioinformatics methods to sequences
• parsing data tables
• querying the resulting databases
• Web interface
• No static HTML pages required
• DNA and Protein viewers make direct access to the
  SQL tables
• Implementation and system requirements
• Perl 5, and C for graphical viewer
• Performance
• parallel capabilities

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Schema
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Bioinformatics Method

• Overview of the PEDANT processing pipeline
• identification of coding regions and various
  analysis genetics elements
• homology search
• detection of protein motifs, prediction of
  secondary structure and other protein features
  and sensitive fold recognition
• automatically attributed to pre-defined
  functional categories
• Prediction of genes and other genetic elements
• Table 1
• choose one of 15 genetic codes
• http//www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wp
  rintgc?modec
• Functional and structural categories
• similarity search PSI-BLAST(Position-Specific
  Iterated BLAST)
• special datasets MIPS, COG, PROSITE, PFAM and
  BLOCKS
• significant matches of PIR annotations,
  keywords, enzyme classification and superfamily
  information
• with significant relationship of PDB, secondary
  structure information STRIDE(upper case),
  PREDATOR(lower case)
• low complexity region, membrance regions, coiled
  coils and signal peptides
• comparison of SCOP with IMPALA

functional
structural
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Table 1
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Bioinformatics Method-Cont.

• Yeast biological role categories
• first system of biological role of categories
  E.Coli
• MIPS advanced hierarchical functional catalogue
  (Yeast)
• Multidimensionality-proteingene is MM
• automated assignment to MIPS is first
  approximation, will be refined by manual
  annotation
• Distribution of ORFs
• Visualization
• a integrated, hypertext-linked protein report
  with calculated parameters and sequences as
  reference for further manual annotation
• Protein report page

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Distribution of ORFs
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Protein report page
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Bioinformatics Method-Cont.2

• Automatic versus manual annotation
• Problem of error propagation
• erroneous annotation by human error and spurious
  similarity hits
• with filtering algorithms and domain structure ?
• quality improvement of manual review of human
  experts !
• Manual annotation
• Catalogue independent
• Flexibility first place in higher category and
  later step move to the finer categories
• 528 categories 20 main categories and 6 levels
• confidence levels reject, low, medium,
  high and default is auto
• Data release management
• new release data can be intelligently merged with
  existing data pool
• transfer manual annotation between subsequent
  data release
• manual field yes or no and default is no
  initially
• example a PFAM domain identified in new release
  ORF is manual no and conf auto

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Manual annotation transfer

• Two contigs fuse to one

• Gene boundary change

• Appears new gene

• Two genes fuse to one contig

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The PEDANT Genome Database

• Annotation of publicly available completely
  sequenced and unfinished genomes
• Genome annotated by MIPS
• Completely sequenced and published genomic
  sequences
• Unfinished and/or unpublished genomics sequences
• gene prediction by ORPHEUS, allow large overlaps
  between ORFs
• PEDANT as a structural genomics resource-0.3M
  proteins
• class-based approach, cost-saving
• (i)non-redundant protein sequence databases
• (ii)PSI-BLAST search with SCOP against (I) abd
  saving resulting profiles
• (iii)construct a SCOP profile library using
  IMPALA
• (iv)IMPALA search with each genomic sequence
  against SCOP library
• same procedure for nr PDB sequence database
• performance of IMPALA
• Cross-genome comparison
• treat each genome as an individual contig creat
  cross-genome datasets without any modification
• 44 genomes

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Performance of IMPALA
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Applications

• Arabidopsis thaliana chromosome IV
• 3744 predicted protein coding genes
• roughly 30 are known proteins or strongly
  similar to known proteins
• multi-cellular organisms has higher all-alpha and
  smaller mixed alpha/beta structural domains ratio
  to unicellular species
• Assembled human transcripts
• human UniGene subjected PEDANT analysis, compare
  over 75000 contigs
• this MySQL DB is close to 8GB
• acceptable query time show the suitability of
  PEDANT for large-scale EST sequencing projects
• Analysis of the GroEL substrates
• GroEL a common E.Coli chaperonin
• structural motif common in 52 substrates relying
  on GroEL for folding in vivo two or more
  alpha/beta domains involving buried beta-sheets
  with large hydrophobic surfaces--easy aggregation

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Classification of predicted genes

• Classification by the degree of homology to
  functionally characterized proteins based on
  BLAST scores

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Summary and Outlook

• PEDANT is a useful tool for genome annotation and
  bioinformatics research
• It can automated and manual assignment of gene
  product to functional and structural categories
• extensive hyperlinked protein report and advanced
  viewers
• Outlook
• better decision rules need to be employed
• manually annotate predicted genetics eelments(ex.
  LTRs)
• supporting Oracle RDBMS
• automatic gene prediction pipeline for higher
  eukaryotes
• interactive capabilities