Bioinformatics lecture

Question 1

The extent to which two sequences are the same

Answer 1

Identity

Question 2

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

Answer 2

Alignment

Question 3

The relatedness of sequences

Answer 3

Similarity

Question 4

A fixed set of commands in a computer program

Answer 4

Algorithm

Question 5

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

Answer 5

Gap

Question 6

Similarity attributed to descent from a common ancestor

Answer 6

Homology

Question 7

The sequence presented for comparison with all other sequences in a selected database.

Answer 7

Query

Question 8

The genetic sequence database sponsored by the National Institutes of Health.

Answer 8

GenBank

Question 9

describes the number of matches
to the query by chance when searching a database of a
particular size.

Answer 9

E- value (Expect value)

Question 10

study on evolutionary relatedness among species by comparing homologies and differences in gene
sequences

Answer 10

Phylogenetics

Question 11

• A field which uses computers to store and analyze
  molecular biological information.
• application of tools of computation and analysis to the capture and interpretation of biological data.

Answer 11

BIOINFORMATICS

Question 12

• Allow the storage and management of large biological data sets
• Data is being generated at a much greater pace than its
  analysis (Human Genome Project)

Answer 12

CREATIO OF DATABASES

Question 13

Determine relationships among members of large data users

Answer 13

DEVELOPMENT OF ALGORITHMS AND STATISTICS

Question 14

• Transcriptomics
• Microbiomics
• Metabolomics
• Genomics
• Proteomics

Answer 14

BRANCHES OF BIOINFORMATICS

Question 15

• Retrieving DNA sequences from databases
• Computing nucleotide compositions
• Identifying restriction sites
• Designing polymerase chain reaction (PCR) primers
• Identifying open reading frames (ORFs)
• Predicting elements of DNA/RNA secondary structure
• Finding repeats
• Computing the optimal alignment between two or more DNA
  sequences
• Finding polymorphic sites in genes (single nucleotide
  polymorphisms, SNPs)
• Assembling sequence fragments
• Creation and visualization of 3D structure models for
  biological molecules of significance.

Answer 15

BIOINFORMATICS APPLICATIONS

Question 16

• Microbial genome applications
• Molecular medicine
• Personalized medicine
• Gene therapy
• Drug development
• Antibiotic resistance
• Evolutionary studies
• Waste cleanup
• Biotechnology
• Climate change studies
• Alternative energy sources
• Crop improvement
• Forensic analysis
• Bio-weapon creation
• Insect resistance
• Improve nutritional quality
• Veterinary science

Answer 16

BIOINFORMATICS APPLICATIONS IN VARIOUS FIELDS

Question 17

THREE EARLIEST DNA SEQUENCE AND PROTEIN DATABASES

Answer 17

• DDBJ (DNA DataBank of Japan)
• EMBL (European Molecular Biology Lab)
• Genbank (USA)

Question 18

• Contain original data in the form of primary sequence data
  or structural data as submitted by the scientific community.
• Examples: GenBank, EMBL, DDBJ, SWISS-PROT and PIR

Answer 18

PRIMARY DATABASES

Question 19

Contain information that has been
process and derived from the raw data available in primary
database

Answer 19

SECONDARY DATABASES

Question 20

• A way of rearranging sequences of DNA, RNA or protein to identify regions of similarity.

Answer 20

SEQUENCE ALIGNMENT

Question 21

To understand functional, structural, or
evolutionary relationships between the sequences

Answer 21

identify regions of similarity

Question 22

TYPES OF SEQUENCE ALIGNMENT

Answer 22

• Pairwise - compare two sequences
• Multiple- compare more than two sequences

Question 23

compare more than two sequences
o MUSCLE
o MAFFT
o CLUSTAL Omega

Answer 23

Multiple

Question 24

compare two sequences
o EMBOSS WATER
o BLAST

Answer 24

Pairwise

Question 25

Matching the residues (bases or amino acids) of two sequences across their entire length o matches the identical sequences o The two sequences are treated as potentially equivalent

Answer 25

Global alignment

Question 26

matching of two sequences from regions which have more similarity with each other o The two sequences may or may not be related o Purpose ▪ To see whether a substring (a part) in one sequence aligns well with a substring (a part) in the other sequence o Applications: ▪ Searching for local similarities in large sequences (e.g., newly sequenced genomes) ▪ Looking for conserved domains of motifs in two proteins

Answer 26

Local alignment

Question 27

multiple sequence alignment tool that arranges the sequences of DNA, RNA or protein to identify regions of similarity

Answer 27

MUSCLE

Question 28

* finds regions of local similarity between sequences. * the amino acid sequences of proteins or the nucleotides of DNA sequences. * compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. * can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Answer 28

- BLAST BASIC LOCAL ALIGNMENT SEARCH TOOL (BLAST)

Question 29

* In BLAST o you supply one or more query sequences and it compares nucleotide or protein sequences to sequence databases * In a multiple alignment o you supply multiple sequences to be aligned to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences

Answer 29

BLAST DIFFER FROM MULTIPLE SEQUENCE ALIGNMENT

Question 30

you supply one or more query sequences and it compares nucleotide or protein sequences to sequence databases

Answer 30

BLAST

Question 31

you supply multiple sequences to be aligned to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences

Answer 31

multiple alignment