BIOINFORMATICS

BIOINFORMATICS

is a combination of information, technology, and molecular biology

BIOINFORMATICS

It is being used largely in the field of human genome research

BIOINFORMATICS

is also used to store and organize the different discovery in the sequence which will be stored in the software

BIOINFORMATICS

It can also used in understanding diseases, new molecular targets, drug discovery, etc

BIOINFORMATICS

The study of how information is represented and transmitted in biological systems, starting at the molecular level

BIOINFORMATICS

is the merger of biology with information technology

COMPUTATIONAL BIOLOGY

Bioinformatics dedicated specifically to handling sequence information is a form of ____?

BIOINFORMATICS

also used to store and organize large amount of data into databases such as those used in clinical sequence analysis

BIOINFORMATICS

used due to vast amount of data arising from the sequence discovery.

BIOINFORMATICS

the science of computer technology and developing computer databases to facilitate biological research.

Standard expression of sequence data

is important for the clear communication and organized storage of sequence data

• Interpretation of sequence variants

• Used in epidemiology to speciate organisms or to find homologies within or between species

• Identification of new sequences

• Useful for test and primer design

Uses of Sequence Information:

Pneumocystis jirovecii or Pneumocystis carinii

was first thought to be a protozoan that is present in the sputum, but it doesn’t align with the protozoan sequence; it matches with the sequence of a fungi

NCBI

Commonly used database

SEQUENCE INFORMATION

includes the principles, practical aspects, and structural analysis

Polymorphic or heterozygous sequences

are written as consensus sequences with proportional representation of the polymorphic bases

International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology (IUB)

have assigned a universal nomenclature for mixed, degenerate, or wobble bases

Consensus Sequences

if there is a mutation in the heterogeneous sequences, there may be more than 1 base or mix bases at the same position in the sequence.

A, G

symbol: R

bases: ??

Mnemonic: PURINE

C, T

symbol: Y

bases: ??

Mnemonic: PYRAMIDINE

G, T

symbol: K

bases: ??

Mnemonic: KETO

A, C

symbol: M

bases: ??

Mnemonic: AMINO

C, G

symbol: S

bases: ??

Mnemonic: 3 H BONDS

A, T

symbol: W

bases: ??

Mnemonic: 2 H BONDS

A, C, T

symbol: H

bases: ??

Mnemonic: NOT G

C, G, T

symbol: B

bases: ??

Mnemonic: NOT A

A, C, G

symbol: V

bases: ??

Mnemonic: NOT T

A, G, T

symbol: D

bases: ??

Mnemonic: NOT C

A, C, G, T

symbol: N

bases: ??

Mnemonic: ANY

UNKNOWN

symbol: X, ?

bases: ??

Mnemonic: A or C or G or T

DELETION

symbol: O, -

bases: ??

Basic Local Alignment Search Tool

BLAST

GENE SEQUENCE

FASTA format =

ARRANGED

GenBank =

Basic Local Alignment Search Tool

System used for homology searches

Basic Local Alignment Search Tool

searches GenBank in National Center for Biotechnology Information (NCBI)

Basic Local Alignment Search Tool

Useful in epidemiology too. You can also confirm bacteria with the same genus through their DNA sequence.

Basic Local Alignment Search Tool

uses GenBank which is also a database for all DNA sequences that were discovered.

Basic Local Alignment Search Tool

is a tool used to aligned 2 sequences

Basic Local Alignment Search Tool

Comparing gene and protein sequences against others in public databases

Basic Local Alignment Search Tool

is a set of sequence comparison algorithms used to search databases for optimal local alignments to a query

Basic Local Alignment Search Tool

It breaks the query and databases sequences into fragments and seeks matches between them

Basic Local Alignment Search Tool

is a computer algorithm that is available for use online at the National Center for Biotechnology Information (NCBI) website and many other sites

Local Alignment

finding similarities on a specific region of a DNA.

Global Alignment

finding similarities from one end to another end, whether they are matching or mismatching.

Basic Local Alignment Search Tool

is the most widely used program in the Bioinformatics

FASTA, GENBANK FORMAT

Input sequences in either of these 2 formats

HTML, plain text, and XML formatting

BLAST output can be delivered in a variety of formats. These formats include ___?

Expect value (E)

is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size

OUTPUT

shows all the records matching the query

• Most of the time, it is in HTML format

mismatching

the higher the background noise, the higher the _____ sequence

matching

The lower the E, the lower the background noise, the higher the ___ sequence?

match

E value = 10-12 = ?

Nucleotide BLAST

sequences of the DNA

Protein BLAST

sequences of the amino acids (sequences of the amino acids were also made from the information of the DNA)

High Scoring Segment Pair (HSP)

local alignment used for aligning 2 DNA without a graph

High Scoring Segment Pair (HSP)

We have match, mismatch, and a gap – all of these have a score.

match

= +2

mismatch

= -2

gap

= 0

HSP

The higher the ___, the higher the amount of match.

• EMBL

• GenBank

• DDBJ (DNA Data Bank of Japan)

PRIMARY BIOLOGICAL DATABASE OF NUCLEIC ACID?

• PIR

• MIPS

• SWISS-PROT

• TrEMBL

• NRL-3D

PRIMARY BIOLOGICAL DATABASE OF PROTEIN?

PRIMARY BIOLOGICAL DATABASE

Also known as Archival Database

GenBank

best for nucleic acid, you can also find protein sequences here.

FASTA

stands for fast-all” or “FastA”

FASTA

It was developed by W.R. Pearson and Lipman and this algorithm can be accessed from EBI site

FASTA

It was the first database similarity search tool developed, preceding the development of BLAST

FASTA

The alignment in diagonals is then refined

FASTA

Finds regions of similarity by first breaking the sequence into short subsequences, then searching for diagonals with highest density of words that match

FASTA

Its fast but is not guaranteed to find the best alignment, it may miss matches

FASTA

Its fast but is not guaranteed to find the best alignment, it may miss matches

FASTA

gives better results for nucleotide sequences than protein

FastP

is for protein sequences

FASTX and FASTY

compares DNA query to a protein database.

TFASTA

compares a protein query to a DNA database.

FASTA format

is a text-based format that represents either the nucleotide sequence or the protein sequence in which that bases or base pairs are represented using a single letter code.

FASTA

can be used for both Local and Global Alignment

FASTA, BLASTA

• to infer relationship between sequences,

• to identify members of the gene families

• as a searching tool for the matching sequences

FASTA GRAPH

simple technique. You just have to find similarities, mismatching, gap, by scoring and tracing back to find the local similarities (or even global similarities).

LOCAL ALIGNMENT

write only the parts of the DNA sequence that are similar or matching.

GLOBAL ALIGNMENT

write both matching and mismatching from end to end of the DNA sequence.

GENBANK FILE FORMAT

Genetic sequence database sponsored by NIH in USA

PubMed

searching tool for journals

SWISS-PROT FILE FORMAT

Protein database sponsored by Medical Research Group of UK (Europe)

• Basic Local Alignment Search Tool (BLAST)

• Gene Recognition and Assembly Internet Link (GRAIL)

• FAST-All derived from FAST-P (protein)

• FAST-N (nucleotide) search algorithms (FASTA)

• Phred

• Polyphred

• Phragment Assembly Program (Phrap)

• The Institute for Genomic Research (TIGR Assembler)

• Factura (Factura)

• SeqScape (SeqScape)

• Assign

• Matchmaker

SOFTWARE PROGRAMS USED TO ANALYZE AND APPLY SEQUENCE DATA

Basic Local Alignment Search Tool

Compares an input sequence with all sequences in a selected database

Gene Recognition and Assembly Internet Link (GRAIL):

Finds gene-coding regions in DNA sequences

FAST-All derived from FAST-P (protein) and FAST-N (nucleotide) search algorithms (FASTA)

Rapid alignment of pairs of sequences by sequence patterns rather than individual nucleotides

Phred

Reads bases from original trace data and recalls the bases, assigning quality values to each base

Polyphred

Identifies single nucleotide polymorphisms (SNPs) among the traces and assigns a rank indicating how well the trace at a site matches the expected pattern for an SNP

Phragment Assembly Program (Phrap)

Uses user supplied and internally computed data quality information to improve accuracy of assembly in the presence of repeats

The Institute for Genomic Research (TIGR Assembler)

Assembly tool developed by TIGR to build a consensus sequence from smaller-sequence fragments

Factura

Identifies sequence features such as flanking vector sequences, restriction sites, and ambiguities.

SeqScape

Mutation and SNP detection and analysis, pathogen subtyping, allele identification, and sequence confirmation

Assign

Allele identification software for haplotyping

New primer or probe

sequence query the primer or probe sequence to confirm that it belongs to the correct species and is not duplicated in multiple places in a genome

misprimes and off-target products

Primers and probes with multiple potential binding sites will produce ??

query

We have to ___ first the primer to confirm if there is similar DNA or if we can anneal it to a similar DNA.

PRIMER DESIGN

Also used to check the size of the amplicons