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Bioinformatics. – a definition ?. The design , construction and use of software tools to generate , store , annotate , access and analyse data and information relating to Molecular Biology. OR. Biologists doing “stuff” with computers?.

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Bioinformatics

– a definition ?

The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology

OR

Biologists doing “stuff” with computers?

Here we consider the use of Bioinformatics tools rather than their design and construction

Here we consider the access and analysis of data and information items rather than their generation, storage or annotation



Primary DNA Sequence Databases

Original submission by experimentalists

Content controlled by the submitter


Primary Protein Sequence Databases

Protein knowledgebase

consists of two sections:

  • Swiss-Prot, manually annotated, reviewed.

  • TrEMBL, automatically annotated,not reviewed.


Derivative Databases

Built from primary data

RefSeq

non-redundant

richly annotated

DNA, RNA, protein

diverse taxa

Submission by experimentalists

Controlled by the submitter

akin to the review literature

akin to the primary

research literature


Derivative Databases

Protein domains, motifs, families

Protein domains/families represented as alignments and HMMs

Derived primarily from UniprotKB and Genpept

Aligned protein domains and consensus sequences

Derived automatically from UniprotKB

Conserved “blocks” of protein domain alignments

Derived from a subset of UniprotKB

Manually curated models for several hundred protein domains

Derived from proteins from completely sequenced genomes


Derivative Databases

Protein domains, motifs, families

Protein motifs/domains represented as Patterns and/or HMMs

Both derived from UniprotKB/Swissprot

Patterns are for highly conserved short regions. Example:

R-P-C-x(11)-C-V-S

HMMs are for less conserved longer regions.

Often there will be pattern(s) and an HMM for one domain.

HMM matches

Pattern matches


Derivative Databases

Protein domains, motifs, families

Representations of domains by motif patterns (fingerPRINTS)

Derived from UniprotKB

Each FingerPrint is compose of a series of conserved regions (motifs)

A match with a FingerPrint is thus an order set of motif matches


For example:

PAX6_HUMAN

matching the

Paired Box,

4 motif, Fingerprint


Database Access

Each database must have software to enable searching

Either by text term against annotation

And / Or by data comparison

Database inquiry by text search:

Sequence Retrieval System – SRS

Searching annotation by text match

Implemented in many places

Follows links between databases

Can allow in situ analysis of matches


Text Search of Annotation

All the databases of the NCBI at one time


Text Search of Annotation

All the databases of the EBI at one time


Database Access

Database inquiry by data comparison:

Sequence databases

BLAST - for sequence databases, DNA or Protein

Implemented in very many places

Most notably at the NCBI

Protein domain, motif, family databases

Each database has a customised search tool

To search all databases is a lot of work!


Database Access

Interpro is a consortium of member databases

Interpro defines protein families, domains, regions, repeats and sites according to matches against member databases

Interpro enables any subset of member databases to be searched together



Genome databases

EBI / Sanger Institute


Levels of access to Ensembl data

Web Browser – One gene inquiry

Web constructed database query

Multi-gene inquiry/data retrieval

PERL libraries to construct customised database queries

The Ensembl Perl API

Customised inquiries – requires PERL programming experience


Towards unification of transcript prediction

The Consensus CDS (CCDS) project

A collaboration

A standard set of gene annotations



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