Bioinformatics

The tblastn database is used to search: A. A protein database using a protein query B. A translated nucleotide database using a protein query C. A nucleotide database using a nucleotide query D. A protein database using a translated nucleotide query

B

Which of the following is a nucleotide database? A. NCBI B. ExPASSY C. Swiss-Prot D. UniProt

A

T/F Many stop codons found together in a DNA sequence suggests the presence of an ORF

False and ORI should not contain any stop codons

T/F A BLAST search can only be performed using a bare sequence, which consists of lines of sequence data containing nucleotides or amino acids

False it can also use FASTA seq and identifiers such as accession numbers

T/F The BLASTP program is used to search a nucleotide database using a protein query

False it is used to search a protein database using a protein query

T/F Horizontal gene transfer between bacterial species makes it easier to establish relationships among bacteria based on their DNA sequences

False it makes establishing relationships more difficult bc it is hard to identify which bacterium piece of DNA originally belonged to

T/F The gene prediction software can analyze a given DNA sequence in only one reading frame

False there are 6 reading frames in which DNA can be read

T/F The use of Open Reading Frames (ORF) to analyze genomic DNA sequences is most effective with eukaryotic genome

False this is in prokaryotes

A. The amount of similarity between DNA or amino acid sequences from different sources B. The accuracy with which alignments are performed during a database search C. The criteria needed to determine how fast a database search will occur D. The technique used to compare the degree of horizontal gene transfer between species

A

All are applications of bioinformatics EXCEPT: A. Construction of family trees B. Research of gene and protein functions C. Compare and identify homologous genes D. Store all genetic information with complete public availability

A

Which of the following statements describes functional annotation? A. Attaching biochemical roles to genomic elements B. Identification of location of regulatory motifs C. Identification of ORFs and their localization D. Identification of coding regions E. Identification of gene structure

A

Which of the following statements does NOT represent a goal of the human genome project? A. Determination of the genetic variants that have frequencies of at least 1% B. Determination of the sequence of nucleotides in the human DNA C. Identification of all the genes in human DNA D. Storage of information generated in a publicly accessible database

A

Which of the following techniques would be the quickest in sequencing a very large piece of genomic DNA? A. Hierarchical shortgun sequencing B. Computer automated DNA sequencing with fluorescently labeled nucleotides C. Traditional Dideoxy sequencing with fluorescently labeled nucleotide D. Traditional Dideoxy sequencing with radioactively labeled nucleotide

A

Which of the following techniques would be valuable in identifying microdeletions in metaphase chromosomes or interphase chromatin strands? A. FISH B. Whole Chromosome painting C. Whole chromosome specific DNA probes D. SNP array

A

Which of the following techniques would not be useful for the detection of multiple gene transcriptional changes? A. Southern Blot B. Macroarrays C. Microarrays D. Northern Blot E. PCR-based analysis F. SAGE G. MPSS

A

A researcher applied the following steps in his enquiry: (1) Isolate mRNA from a tumour, (2) Make cDNA from the isolated mRNA (3) Extract a small chunk of sequence from a defined position of each cDNA molecule, (3) Link these small pieces of sequences together to form a concatemer, (4) Sequence concatemerized tags(5) Process this data with a computer to count the small sequence tags. Which technique do these steps describe? A. PCR B. SAGE C. Northern Blotting D. RFLP E. Tiling array F. Microarray G. MPSS H. Macroarray

B

Two groups of bacteria were taken from a sample and after their DNA was isolated, the samples were compared. It was found that most of their DNA was different in composition, but they contained some sequences which were similar. Of the following choices below, which of these is MOST LIKELY to be true? A. They may be found close together on a phylogenetic tree B. Some genes may have been shared via horizontal gene transfer C. The two bacteria are closely related D. They were derived from the same parent colony

B

What does "BLAST" mean? A. Bovine Localized Allele Specific Tracer B. Basic Local Alignment Search Tool C. Basic Local Alignment Sequence Tool D. Bioinformatic Level Alignment Specific Tool

B

Which of the following techniques would be fastest in sequencing a very large piece of genomic DNA? A. Hierarchical shortgun sequencing B. Next Generation Sequencing C. Computer automated dideoxy sequencing with fluorescently labelled nucleotides D. Traditional Dideoxy sequencing with fluorescently labeled nucleotide E. Traditional Dideoxy sequencing with radioactively labeled nucleotide

B

Which of these statements best describes the structure of the FASTA format used for a BLAST database search? A. Lines of sequence data (represented by single letters for each amino acid) B. A single-line description followed by sequence data C. One-word identifiers that may contain numbers D. A specific sequence of amino acids that tells the database to start a search

B

T/F Gene prediction software is used to identify genes with short DNA sequence

False DNA sequences need to be long

Which of the following programs is an example of a gene prediction software? A. BLASTX B. ClustalW C. ORF Finder D. BLASTP E. BLASTN

C

The alignment of DNA sequences from several different organisms gives information about: A. The function of the genes associated with those DNA sequences B. The potential genes that can be read from the sequence C. Regions that contain the most similarity between organisms D. Regulatory regions and intronic sequences

C

When conducting a BLASTN search, you are searching/analyzing what type of information? A. Protein sequence data B. Amino acid sequence data C. Nucleotide sequence data D. Phenotypic data

C

Which databank will you choose to analyse this sequence: MASPFRAV A. EMBL B. DDBJ C. PIR D. NCBI

C

Which of the following substances/enzymes would not be contained in a DNA sequencing reaction? A. Primer B. DNA polymerase C. RNA polymerase D. Labeled dideoxynucleotides E. Deoxynucleotides F. Buffers

C

You are performing research which involves the use of bioinformatics databases and search tools. If you wanted to compare sequence alignments between many different organisms to search for phylogenetic relationships, which of the following would be most appropriate to use?

Clustal w

Which of the following terminologies defines a sequence of amino acid or nucleotide used in a BLAST search? A. DNA sequence B. Annotation C. ORF D. Score value E. Query sequence F. Alignment

E

In which of the following techniques is cDNA fragments cloned onto micro-beads sequenced? A. RFLP B. Macroarray C. Tiling array D. MPSS E. Microarray F. SAGE G. Northern Blotting H. PCR

D

The E-value refers to: A. The sequence used to perform a search across different databases B. The diagram showing regions of sequences that are compared C. The amount of similarity between the query and the search result D. The number of alignments that have scores better than or equal to alignment scores occurring by chance

D

The MASCOT database is used for: A. Searching for peptide fingerprints B. Sequence Query C. MS/MS Ion Search D. All of the above

D

Which of the following information from the genome may be identified by aneuploid screen test? A. A nucleotide pair substitution B. A single nucleotide polymorphism C. An individual's hemoglobin genotype D. An extra chromosome

D

Which of the following technologies is best suited for the analysis of mRNA? A. Eastern Blot B. Southern blot C. Far-Eastern Blot D. Western blot E. Northern blot

E

__ _____ The number of different alignments with scores that are equivalent to or better than alignment scores that are expected to occur by chance

E value

____ Nucleotide Sequence Database that is equivalent to the US Gen Bank

EMBL

_____ The new Swiss Institute of Bioinformatics Resource Portal that provides access to scientific databases and software tools in different areas of life sciences

ExPASY

______ _____ obtaining biological information from unprocessed sequence data to create a labeled genome

Genome annotation

___ NIH genetic sequence database comprised of DDBJ, EMBL and GenBank

NCIB

___ Grew out of the Atlas of Protein Sequence and Structure which was edited by Margaret Dayhoff

PIR

________ _____ A sequence to be used in a BLAST search that is made up of amino acids or nucleotides that can be either in FASTA format, Bare sequence, or an identifier such as Accession number

Query sequence

____ ____ Major European protein sequence database, from the Swiss Institute of Bioinformatics

Swiss prot

T/F ) Multiple Alignment software like CLUSTAL W and COBALT are used by scientists to study phylogenetic relationships between species

True

T/F BLAST program searches a nucleic acid or amino acid database to find matching or similar sequences to the one being tested

True

T/F The MASCOT Search Engine integrates different methods of database searching and can search for peptide fingerprints, sequence query and MS/MS Ions

True

T/F The method of using Open Reading Frames to detect genes is called ab initio because it attempts to predict genes based on knowledge and understanding of gene structure

True

___________ A measure of the quality of the alignment between the query sequence and the search results

alignment

A diagram that shows the inferred evolutionary relationships among various biological species is called: A. A Punnett square B. A phylogenetic tree C. A genetic cross D. A family tree

b

When performing a bioinformatics database search using a query, the best results should have a: A. Low Score and Low E-value B. High Score and High E-value C. High Score and Low E-Value D. None of the above

c

Which of the following would NOT suggest the presence of an Open Reading Frame (ORF)? A. A start codon B. An in-frame stop codon C. Stop codons close together D. A Shine-Dalgarno sequene

c

T/F A diagram that shows the inferred evolutionary relationship among various biological species is called a family tree

false it is a phylogenetic tree

_______ _______ attaching biological information such as regulation biochemical function and expression to genomic elements

functional annotation

____ _____ A measure of the quality of the alignment between the query sequence and the search results

score value

_____ ______ identifying genomic elements such as genes and other important sequences like coding regions and regulatory motifs

structural annotation

_________ Single protein database that combines information from major international databases

uniprot