Bioinformatics and Computational Molecular Biology

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Bioinformatics and Computational Molecular
Biology
-midterm presentation

• Team members
• B929202031 ???
• B929020278 ???

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Introductions!
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(No Transcript)
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Introductions(1/3)

• Biozon is a unified biological resource on DNA
  sequences, proteins, complexes and cellular
  pathways.
• emphasize on protein DNA characterization and
  classification
• The goal of Biozon
• for easily integrating with other data types and
  existing future databases
• The Biozon database was developed by
• Yona's lab at the Department of Computer Science
  in Cornell University

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Introductions(2/3)

• Biozon is built upon preexisting databases

DNA Sequence Databases- GenBank, UniGene
Protein-Protein Interactions- BIND, DIP
Pathways- KEGG
Biozon
Protein Sequence Databases- SWISSPROT/TrEMBL, PIR
Gene Expression- BodyMap
Protein Structure Databases- PDB, SCOP
Gene Ontology- Gene Ontology Consortium
Domains- InterPro
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Introductions(3/3)

• Biozon Data Set

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Searches!
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Search Overview

• Biozon data is searchable through three modes
• quick search
• searches through the definitions of all data
  objects (logical word available!)
• simple search
• search for all entities of a certain type that
  match a specific keyword or gene name.
• complex search
• searches for involving multiple data types
• Fuzzy Search

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Mode1-Quick Search
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Search Pre
edges indicate a relationship between two nodes

• Start a new search

Main data types in Biozon
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Mode3-Complex Search (1/2)
To begin a search, select the type of object you
are searching for.
Select an object to add to the query, relating it
to one of the objects already defined in the
query.
After selecting the type of object (structures,
in this example), enter any constraints you may
have on the object's attributes.
After adding any object to the query, fill in any
constraints that are to be applied to that
particular object.
Enter any constraints on the newly added object.
The relative ranks of the objects in the result
set are shown as red bars. The longer the bar,
the higher the rank.
Add another object to the query
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Mode3-Complex Search (2/2)
-Fuzzy Search
The results are colour-coded to indicate the type
of similarity that was used to find the
particular result. A legend is at the bottom of
the page .
any results that were attained by using
similarity are marked with a color square on the
extreme left.
Also accessible from the provenance page is the
profile information of any object instance in the
query tree. To view, click on its identifier.
To make a particular search fuzzy, select at
least one of the checkboxes at the end of the
protein search form page.
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Tools!
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Analysis Tools

• Submit for analysis
• Sequence
• Profile (under structure)
• Structure (under structure)
• More tools
• Predict the domain-structure of a protein
• Assess similarity measures for expression
  profiles
• Analyze EST sequences

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Sequence Analysis
gtgi11496891refNP_000662.2 class III alcohol
dehydrogenase 5 chi subunit Homo sapiens
MANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAY
TLSGADPEGCFPVILGHEGA GIVESVGEGVTKLKAGDTVIPLYIPQCGE
CKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY
MGTSTFSEYTVVADISVAKIDPLAPLYKVCLLGCGISTGYGAAVNTAKLE
PGSVCAVFGLGGVGLAVIMG CKVAGASRIIGVDINKDKFARAKEFGATE
CINPQDLSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALE
ACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPK
LVSEYMSKKIKVDEFVTHNL SFDEINKAFELMHSGKSIRTVVKI
H.sapiens ADH5 -gt NP_000662.2 -gt FASTA
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Analysis Tools

• Submit for analysis
• Sequence
• Profile (under structure)
• Structure (under structure)
• More tools
• Predict the domain-structure of a protein
• Assess similarity measures for expression
  profiles
• Analyze EST sequences

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EST Sequence Analysis
Non-redundant definitions of proteins mapped to
ID
GO terms and Swiss-Prot keywords classifying
proteins mapped to ID
"yes" if ID is mapped to a protein involved in an
interaction, "no" otherwise
User uploaded GenBank accession number or GI
number
AI834965 AI834966 AI834967 AI834969 AI834970
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Download!
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Download page
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Thanks for your attention!