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Bioinformatics. Flashcards

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1
Q

Define the DNA reading frame?

A

Each strand of DNA has 3 possible open reading frames where the strand is read in codons.

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2
Q

How many reading frames does a DNA molecule have?

A

6.

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3
Q

Define genome annotation?

A

The process of obtaining biological information from unprocessed, sequenced genetic data.

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4
Q

Define the MASCOT search engine?

A

A bioinformatic database.

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5
Q

What is bioinformatics?

A

The process of solving biological problems by utilising information stored on computer databases.

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6
Q

What is used in bioinformatics to increase biological understanding?

A

Biological databases.

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7
Q

Who coined the term bioinformatics in 1979?

A

Paulien Hogeweg.

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8
Q

How has bioinformatics helped the field of medicine?

A

By allowing us to compare biological processes in healthy and diseased bodies.

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9
Q

How is the information in bioinformatic databases used to help advance medicine?

A

The information has been collected from past patients and can be used to diagnose the same disease in others.

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10
Q

What kind of maps has the information from bioinformatic databases helped to create?

A

Genetic maps that show heritable traits.

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11
Q

How can bioinformatic databases help taxonomists classify species?

A

They can store the genome sequences of different organisms.

This allows for comparisons to be made between different organisms.

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12
Q

How has bioinformatics helped law enforcement companies?

A

Police forces use databases to store DNA profiles of convicted offenders making it easier to catch repeat offenders.

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13
Q

How can bioinformatics help molecular biologists conduct their experiments?

A

Primers designs are stored in databases. This allows scientists to easily build a primer.

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14
Q

How has bioinformatics helped pharmacologists?

A

They can use bioinformatics to design new drugs that are personalised for a persons genome.

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15
Q

How has bioinformatics helped farmers?

A

It has helped farmers develop new strains of crops which are disease or pest resistant.

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16
Q

From what biological sources will bioinformatics use data?

A

DNA.

RNA.

Protein.

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17
Q

How can bioinformatics help scientists sequence DNA strands?

A

By storing the information from past DNA experiments, this allows scientists to compare sequences.

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18
Q

How has bioinformatics helped with the study of proteins?

A

The storing of information related proteins allows other researchers to identify the same protein quickly.

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19
Q

What does the storage of information relating to proteins allow scientists to study about how proteins are changing?

A

It allows them to study evolution of proteins and also the mutations that can arise within their structure.

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20
Q

What are 5 ways that bioinformatics can help to study DNA?

A

Analysis of a DNA sequence.

The discovery of new genes.

The discovery of regulatory regions within the DNA strand.

The ability to annotate whole genomes.

To carry out comparative genomics.

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21
Q

The storage of DNA sequences in bioinformatic databses allows scientists to make what comparisons?

A

It allows scientists to compare genome sequences between different people.

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22
Q

What does the comparison of DNA sequences from different people allow for?

A

The detection of areas in the genome that code for genetic diseases such as sickle cell.

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23
Q

How does the study of different DNA strands help pharmacologists?

A

It allows them to develop new drugs that are likely to be absorbed and metabolised by the patient.

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24
Q

How does the storage of different genomes help us to study the physical genome?

A

It helps us find new genes or regulatory regions such as a TATA box or a binding domain for a regulatory protein.

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25
Q

What are 6 factors about RNA that bioinformatics can help study?

A

The different products of RNA splicing.

The expression of different RNA’s in different tissues.

The structure of different RNA’s.

The types of RNA that are produced by a single gene.

The RNA’s that are produced by thousands of genes at the same time.

The creation of specific DNA chips and microarrays for RNA analysis.

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26
Q

Why is it important to store the information that relates to the products of RNA splicing?

A

To know all of the products that can be produced by a single gene.

To know which RNAs are produced in response to an external stimulus.

To build genetic probes and microarrays.

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27
Q

What are 6 factors about proteins that bioinformatics can help with?

A

The identification of protein families.

The identification of various protein domains and regions.

The identification of various protein structures.

The identification of various protein functions.

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28
Q

How is bioinformatics used in the identifcation of proteins?

A

The results from electrophoresis and mass spectrometry are fed into a database for protein identification.

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29
Q

What are the 2 categories if bioinformatic databanks that store information relating to DNA, RNA and proteins

A

Databases that store information relating to nucleic acids.

Databases that store information relating to proteins.

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30
Q

What is GenBank?

A

The NIH genetic sequence database and is part of the International Nucleotide Sequence Database Collaboration (INSDC).

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31
Q

What 3 databanks help to make up the INSDC?

A

The DNA Data Bank of Japan (DDBJ).

The European Molecular Biology Laboratory (EMBL).

The GenBank at NCBI in the USA.

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32
Q

What does the INSDC allow researcher to do?

A

To identify a particular nucleotide sequence by searching through millions of different nucleotides.

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33
Q

In what format is genetic information at the NCBI stored?

A

In a format that displays information about the nucleic acid such as function etc.

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34
Q

What is Uni-prot?

A

A database that combines all of the information from major international databases.

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35
Q

What 5 major databnaks does Uni-prot obtain information from?

A

European Bioinformatics Institute (EBI).

Protein Information Resource (PIR).

Georgetown University Medical Centre (GUMC).

National Biomedical Research Foundation (NBRF).

The Swiss Institute of Bioinformatics (SIB).

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36
Q

What is ExPasy?

A

A tool from the SIB and it provides access to databases and software tools that cover all areas of life sciences.

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37
Q

What does ExPasy stand for?

A

The expert Protein Analysis System.

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38
Q

What is a query sequence?

A

A particular sequence that is chosen by the experimenter and instead into a BLAST search.

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39
Q

What can a query sequence be made up of?

A

Of amino acids or nucleotides.

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40
Q

When is a BLAST search performed?

A

When a researcher wants to discover more information that relates to their query sequence.

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41
Q

BLAST searches require query sequences to be of what length?

A

At least 15 nucleotides or amino acids.

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42
Q

How do scientists perform a BLAST search?

A

They insert the query sequence into a database.

This allows them to compare their sequence to all of the known sequences within the database.

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43
Q

What are the 2 formats that a query sequence can be entered into a BLAST search?

A

The FASTA forma.

The identifier format.

44
Q

What does the FASTA format of a BLAST search consist of?

A

Only the nucleotide or amino acid sequence.

45
Q

How does the identifier format differ from the FASTA format?

A

It contains the sequence with an accession number or gene ID information.

46
Q

What is alignment?

A

The presentation of 2 sequences that can be compared to show the regions of similarity.

47
Q

How is alignment performed?

A

When a researcher compares their query sequence with a known sequence.

48
Q

What is the score value?

A

A term that is used to measure the quality of alignment between a query sequence and the search results.

49
Q

What is the score in the score value usually based on?

A

On the number of nucleotide or amino acid matches between the query sequence and the search results.

50
Q

Does a high score value mean good or bad alignment?

A

The higher the score the better the alignment.

51
Q

What does the score value allow for when selceting matches between search results and the query sequence?

A

For the selection of the best match between the query sequence and the search results.

52
Q

What is the E-value?

A

The expectation value.

It measures the amount of possible outcomes.

53
Q

What does the expectation value highlight?

A

The significance of an alignment.

Many alignments mean that there are many possible outcomes.

A single alignment means there is only one possible outcome.

54
Q

Does a low or high e-value indicate a good match between the query sequence and the search results?

A

The lower the E-Value the better the match.

55
Q

What is a genome annotation?

A

The process of obtaining biological information from unprocessed sequence data.

56
Q

What is the ultimate goal of genome annotation?

A

To create a labelled genome, where biological information is linked to a particular genetic sequence.

57
Q

What will a genome annotated map tell us?

A

Exactly what each gene does.

58
Q

What 2 categories can genome annotation be divided into?

A

Structural and functional annotations.

59
Q

What do strucutral genome annotations attempt to identify?

A

Genomic elements such as the promoter sequence or the TATA box.

60
Q

What 3 things do strucutural genome annotation involve?

A

Researching the structure of genes.

Researching the areas of the genome that code for certain products.

Reaserching the location of regulatory motifs such as the TATA box.

61
Q

What does the results from strucutral genome annotations allow for?

A

The identification of the cis factors that are used in transcription and translation.

62
Q

What do functional genome annotations allow for?

A

To identify the biological functions of genomic products such as proteins.

63
Q

What is the basic tool of genome annotations?

A

The BLAST program which allows us to identify similarities between genes and proteins.

64
Q

What is gene prediction software used for?

A

To identify the genes found in long DNA sequences that code for amino acids and have no STOP-codons.

65
Q

What factor inherent to DNA is used by gene prediction software when identifying genes on an unknown strand?

A

The DNA reading frame which allows for the strand to be read in triplets or codons.

66
Q

How many reading frames does each DNA strand have?

A

3.

67
Q

What does the correct reading frame from a DNA strand tell you about the strand?

A

The knowledge of the amino acid products that are provided by the DNA strand.

68
Q

How many reading frames must gene prediction software evaluate if it is analysing an entire DNA molecule?

A

6 possible reading frames for a DNA molecule as it consists of 2 strands.

69
Q

What happens once the correct reading frame has been interpreted by gene prediction software?

A

We can identify the protein that is created by a gene by using the list of amino acids that are created.

70
Q

What are 2 tools that can help identify the open reading frame?

A

The Open Reading Frame Finder at ORF FINDER or at GEN-scan.

71
Q

What complicates gene prediction software?

A

The fact that most of a genome is made from non-coding DNA.

This means gene prediction software must identify coding DNA from non-coding DNA.

72
Q

What are 10 common features found in coding DNA?

A

The open reading frame.

A start codon.

A stop codon.

A terminator sequence (prokaryotes).

A TATA box (eukaryotes).

A Shine Delgano sequence (prokaryotes).

Kozak sequence (eukaryotes)

A poly-A addition sequence (eukaryotes).

Intron and exon boundaries.

CPG islands.

73
Q

What kind of genome is the ORF very good at analysing?

A

The bacterial genome.

74
Q

Why is the ORF not good for analysing the eukaryotic genome?

A

Because they contain introns and exons that are spliced into and out of mRNA’s that code for proteins.

75
Q

What makes a good ORF?

A

It should begin with a START-codon (a methionine residue) and end with an in frame STOP-codon.

76
Q

How does the presence many STOP-codons that are located close together on an unknown strand affect the ORF?

A

It suggests that an ORF is not present.

77
Q

Why are longer ORFs better than short ORFs?

A

As the longer the ORF, the less likely it is to occur by chance.

78
Q

What does sequence alignment software allow for?

A

Ffor a newly sequenced gene to be analysed to see if it is already known and stored in a database.

79
Q

What are the 2 most popular tools that are used for sequence alignment?

A

BLAST (Basic Local Alignment Search Tool).

FASTA (Fast All).

80
Q

What is the most widely used program in bioinformatics?

A

The BLAST program.

81
Q

What does the BLAST program do?

A

It searches through a database to find matching or similar sequences the one that is being tested.

82
Q

How do results from the BLAST program appear?

A

As high scoring segment pairs (HSPs).

Where the score is the amount of matches between the query sequence and the database sequence.

83
Q

What can we do after the matches have been produced by BLAST?

A

We can evaluate the matches.

84
Q

What is the main idea behind the BLAST tool?

A

To find regions of similarity between the sample sequence and the known sequences from the database.

85
Q

What are local similarities that have been detected by BLAST?

A

Where both sequences have a region of similarity that is based in a single location.

86
Q

What are global similarities that have been detected by BLAST?

A

Where the 2 sequences have regions of similarity all over the sequence.

87
Q

What kind of database is BLAST-P and what kind of query is used to search through the database?

A

A protein database.

A protein query.

88
Q

What kind of database is BLAST-X and what kind of query is used to search through the database?

A

A protein database.

A translated nucleotide query.

89
Q

What is compared via the use of BLAST-X?

A

This method compares the 6-frame translations of DNA to a protein database.

90
Q

What kind of database is tblastn and what kind of query is used to search through the database?

A

A translated nucleotide database.

A protein query.

91
Q

What kind of database is tblastx and what kind of query is used to search through the database?

A

A translated nucleotide database.

A translated nucleotide query.

92
Q

What is compared via the use of tblastx?

A

This method compares the 6 frame translations of a DNA query to the 6 frame translations of a DNA database.

93
Q

Each sequence of tblastx is comaprable to sequences from which other BLAST technique?

A

To BLAST-P sequences.

94
Q

What kind of database is FASTA and what kind of query is used to search through the database?

A

DNA or protein database.

A DNA or protein query.

95
Q

What kind of database is FAST-X and what kind of query is used to search through the database?

A

A protein database.

A translated DNA sequence.

96
Q

What kind of database is TFASTA and what kind of query is used to search through the database?

A

A translated DNA database.

A protein query.

97
Q

What marks the beginning of a query sequence that uses the FASTA format?

A

A single line description that is followed by the lines of sequence data.

98
Q

How is the description line distinguished from the sequence data line in a query sequence in FASTA format?

A

Becuase the description line has a greater than (“>”) symbol in the first column.

99
Q

How many characters should a FAST input have?

A

It should not exceed 80 characters.

100
Q

Can blank lines be entered into the FASTA format?

A

No.

101
Q

What is the input sequence for the BARE format of a BLAST search?

A

Lines of sequencing data without the FASTA definition line.

102
Q

What is the input sequence for the IDENTIFIER format of a BLAST search?

A

They are accession numbers, accession versions or gi’s.

These are sequence ID tags that the database has attached to a particular gene or protein.

103
Q

What is sequence homology?

A

The analysis of DNA sequences from different organisms to determine the evolutionary relationships.

104
Q

What is one flaw to sequence homology?

A

Bacteria can exchange DNA sequences via horizontal gene transfer.

105
Q

What software is often used by scientists to investigate phylogenetic relationships?

A

Multiple sequence alignment software such as CLUSTAL and COBALT.

106
Q

What do taxonomists create to show how closely different organisms are related?

A

Phylogenetic trees.

Molecular Biology. (22 decks)

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