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This quiz contains multiple-choice problems on DNA and genomic sequencing, cDNA libraries of expressed genes, sequence formats and storage, database access program, genome anatomy, comparative genomics, sequence assembly and gene identification.
Using ddATP, the resulting synthesis creates a set of nested DNA fragments, each ending at one as in the sequence through substituting a fluorescent-labelled ddATP. True or false?
True
False
The combined mixture of all labelled DNA fragments is electrophoresed to __ the fragments by __, and the ladder of fragments are scanned for the presence of each of the four labels.
separate, size
separate, pH
assimilate, pH
assimilate, size
When the process is fully automated, many priming sites may be used to obtain sequencing results that give optimal separation of bands in each region of the sequence. True or false?
True
False
To sequence larger molecules, individual chromosomes are purified and broken into __ or larger random fragments, cloned into vectors designed for large molecules.
100-Mb
100-kb
5000-kb
600-kb
Many levels of clone redundancy may be required to build a consensus map because individual clones can have
Rearrangements
Deletions
Two separate fragments
Vectors
An alternative method is to sequence all the subclones, produce a computer database of the sequences, and then have the computer assemble the sequences from the overlaps that are found. True or false?
True
False
Each DNA or protein sequence database entry has much information, including
An assigned accession number(s)
Source organism
Name of locus
Reference number type(s)
BL contains information about the block: xxx is the amino acids in the spaced triplet found by MOTIF upon which the block is based. True or false?
True
False
A sequence can be verified by making an oligonucleotide primer complementary to the distal part of the readable sequence and using it to obtain the sequence of the complementary strand on the original DNA template. True or false?
True
False
Which of the following statements is incorrect regarding READSEQ?
It is an extremely useful sequence formatting program developed by D. G. Gilbert at Indiana University, Bloomington
It was developed at Indiana University, Bloomington
It can recognize a DNA or protein sequence file in any of the formats
It can recognize a DNA or protein sequence file in some particular formats
Which of the following statements is incorrect regarding DNA sequencing methods?
Purified fragments of DNA cut from plasmid/phage clones or amplified by polymerase chain reaction (PCR)
Clones of DNA fragments are denatured to single strands, and one of the strands is hybridized to an oligonucleotide primer
Taq polymerase is quite heat sensitive
New strands of DNA are synthesized from the end of the primer
Which of the following statements is incorrect regarding shotgun sequencing?
When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to overlap
When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to scrutinize
In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths
A large number of reads are then assembled by computer
Which of the following statements is incorrect regarding database types?
Relational databases are more useful in the development of biological databases
The tables in relational database are carefully indexed and cross-referenced with each other, sometimes using additional tables, so that each item in the database has a unique set of identifying features
The relational database orders data in tables made up of rows giving specific items in the database, and columns giving the features as attributes of those items
The two principal types of DBs are the relational and object-oriented databases
Which of the following statements is incorrect regarding the block multiple sequence alignment format?
Identification starts contain a short identifier for the group of sequences from which the block was made and often is the original Prosite group ID
The identifier is terminated by a comma, and “BLOCK” indicates the entry type
AC contains the block number, a seven-character group number for sequences from which the block was made, followed by a letter (A–Z) indicating the order of the block in the sequences
The block number is a 5-digit number preceded by BL (BLOCKS database) or PR (PRINTS database)
Once the correct map is obtained, unique overlapping clones are chosen for sequencing. True or false?
True
False
