Bioinformatics

Margaret O. Dayhoff (1965 1978)

Edited the collection of amino acid sequences compiled in the Atlas of protein sequence and structure by comparison of amino acid sequences by developing computer software for detecting distantly related sequences

NCBI

• Established in USA

• The primary information databank and provider of information

Bioinformatics

• Blends computer science and biostatistics w/ biomedical sciences such as: epidemiology, genetics, genomics, and proteomics

• a combination of biology and informatics

In silico

Bioinformatics is analysis in?

HUMAN GENOME PROJECT

• spurred the rapid rise of bioinformatics as a formal discipline

• Goal: facilitate the management, analysis and interpretation of data from biological experiments and observational studies.

Alignment

Lining up two or more sequences to search for the maximal regions of identity (or similarity) in order to assess the extent of biological relatedness or homology

Identity

The extent to which two sequences are the same

Local alignment

Alignment of some portion of two sequences

Multiple sequence alignment

Alignment of three or more sequences arranged with gaps so that common residues are aligned together

Optimal alignment

The alignment of two sequences with the best degree of identity

Conservation

Specific sequence changes (usually protein sequence) that maintain the properties of the original sequence

Similarity

The relatedness of sequences, the percent identity or conservation

Algorithm

A fixed set of commands in a computer program (stores the bioinformatics)

Domain

A discreet portion of a protein or DNA sequence

Motif

A highly conserved short region in protein domains

Gap

A space introduced in alignment to compensate for insertions or deletions in one of the sequences being compared

Homology

Similarity attributed to descent from a common ancestor

Orthology

Homology in different species due to a common ancestral gene

Paralogy

Homology within the same species resulting from gene duplication

Query

The sequence presented for comparison with all other sequences in a selected database (e.g., NCBI)

Annotation

Description of functional structures, such as introns or exons in DNA or secondary structure or functional regions to protein sequences

Interface

The point of meeting between a computer and an external entity, such as an operator, a peripheral device, or a communications medium

PubMed

Search service sponsored by the National Library of Medicine that provides access to literature citations in Medline and related databases

SwissProt

Protein database sponsored by the Medical Research Council (United Kingdom)

NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION (NCBI)

• Create automated systems for storing and analyzing knowledge about molecular biology, biochemistry and genetics

• Research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules and compounds

• Facilitates the use of databases and software by biotechnology researchers and medical care personnel

• Coordinate efforts to gather biotech information worldwide

Heterozygous mutations

Important in bioinformatics because more than one base or mixed bases at the same position in the sequence

Consensus sequences

A family of sequences with proportional representation of the polymorphic bases

IUB Universal Nomenclature for Mixed Bases

• Made by the International Union of Pure and Applied Chemistry and International Union of Biochemistry and Molecular Biology

• Their base designations in the IUB code are used to communicate consensus sequences and for computer input of polymorphic sequence data

BLAST - Basic Local Alignment Search Tool

• for homology searches

• Searches GenBank (large database maintained by NCBI)

• Nucleic acid or amino acid sequences

• searches for regions of local similarity between protein and nucleotide sequences

E-values

• number of matches to the query

• Decreases exponentially with the quality of the match

• Very low E-values (10-12) associated with perfect match

FASTA

• File extensions: ‘.fasta’ or ‘.fa’ o

• Most widely used formats in bioinformatics o

• Can be a single sequence format or multiple sequence forma o

• The format f when you search it in the blast or other websites, it begins with ‘greater than’ (‘>’) symbol

• Organism origin

• Sequence accession number

• Sequence description, features and comments

• Separated by dash (-), underscore (_) and pipe symbols (|)

FASTA contains:

GenBank File

• Starts with LOCUS and the sequence itself o

• Begins with ORIGIN and ending with double slant (//)

EMBL File

• Used by European Molecular Biology Laboratory (EMBL)

• Begins with an identifier (marked with “ID”)

• Start of sequence: marked by ‘SQ’ and the end by ‘//’ same with the GenBank file

CLUSTAL

• Typical file extension: ‘.aln’ o

• Includes multiple sequences in one file. It is used as an input format for phylogenic algorithms. Format starts with the word “CLUSTAL”

• Each sequence is identified by a name followed by a space and a string of characters. The dashes (-) indicates deletions

NEXUS

• Typical file extension: ‘.nex’ or ‘.nxs’ o

• Begins with the wording “nexus” followed by blocks containing commands. Each block begins with “begin block name” and ends with “end”

PHYLIP

• Typical file extension: ‘.phy’ or ‘.ph’ o

• It begins with a number of sequence in the file followed by the length in base pairs of the alignment. Followed on the next line by the alignment block. Alignment block for each specie

Known

reference sequence

Unknown

query sequence

Global Alignment

• Two sequences to be aligned are assumed to be generally similar over their entire length

• Uses the Needleman-Wunsch algorithm

• Carried out from beginning to end of both sequences

• Compare two genes with same functions (humans vs mouse)

• Compare two proteins with similar functions

Applications of global alignment:

Local Alignment

• Based on Smith-Waterman

• Does not assume that the two sequences in question have similarity over the entire length

• Finds local regions with highest level of similarity between two sequences and aligns these regions without regard for alignment of the rest of the sequence regions. It aligns locally and not the entire sequence

• Input: two sequences may or may not be related

• Goal: see whether a substring in one sequence aligns well with a substring in the other

• Searching for local similarities in large sequences (e.g. newly sequenced genomes)

• Looking for conserved domains or motifs in two proteins

Applications of local alignment:

Pairwise sequence alignment

Used to find the best-matching piecewise (local or global) alignments of two query sequences.

1. Dot Matrix

2. The Dynamic Programming (DP) Algorithm

3. Word or K-Tuple Method

3 Primary Method of Producing Pairwise Alignments:

Dot matrix (Dot plots)

Similar nucleotides of 2 DNA sequences are represented as dots

Dynamic Programming (DP) method

• Introduced by Richard Bellman (1940)

• Useful in aligning nucleotide sequences of DNA and amino acid sequences of proteins coded by that DNA

Word method/K-Tuple method

• Useful in large-scale database searches to find whether there is significant match available with the query sequence

• Used in FASTA and BLAST family

• Identify a series of short, non-overlapping subsequences (words) of the query sequence

1. Blastp

2. Blastn

3. Blastx

4. tBlastx

5. tBlastp

Standard BLAST are of 5 types:

BLASTp

This program compares an amino acid query sequence against a protein sequence database

BLASTn

It compares a nucleotide query sequence against a nucleotide sequence database

BLASTx

It searches the six frame translation products of a nucleotide sequence against a protein database

tBLASTn

It searches a protein sequence against translated nucleotide sequence in the database

tBLASTx

It compares the six frame translations of a nucleotide query sequence against six frame translations of database

Mega BLAST

It is a program optimized for aligning long sequences. It can only work with DNA sequences

PSI BLAST

It stands for position specific iterated BLAST. It is useful for protein similarity search

PHI BLAST

Pattern hit initiated BLAST, it can be used to search for a specific pattern or motif