Lecture 08 - Bioinformatics

Question 1

What is bioinformatics

Answer 1

the collection, classification, storage and analysis of biochemical and biological information using computers especially as applied to molecular genetics and genomics

Question 2

What is the INSDC

Answer 2

international nucleotide sequencing database collective

Question 3

Who makes up the INSDC

Answer 3

DDBJ, NCBI, ENA

Question 4

What is the DDBJ

Answer 4

DNA data bank of Japan

Question 5

What is the NCBI

Answer 5

national center for biotechnology information

Question 6

What is the ENA

Answer 6

european nucleotide archive

Question 7

What is the FASTA format

Answer 7

accession number, identifier, what kind it is, then sequence

Question 8

What is FASTQ used for

Answer 8

next generation sequencing

Question 9

What is found in the GenBank Header

Answer 9

locus, definition, accession, version, keywords, source, references

Question 10

What information is found in the locus

Answer 10

• locus name
• length of sequence
• molecule type
  -genebank division (3 letter code)
• date last modified

Question 11

What is in the definition

Answer 11

a brief description of the sequence (may include source organism and gene name)

Question 12

What is the accession number

Answer 12

a unique identifier for the sequence within the database

Question 13

What is the version number

Answer 13

it denotes any change to the sequence since it was first submitted

Question 14

What is a reference sequence

Answer 14

high quality sequences that the NCBI have curated

Question 15

What is the format for refSeq accession numbers

Answer 15

have an underscore
NM_
NC_
NG_
NR_
NZ_

Question 16

What is the source

Answer 16

free-format information including an abbreviated form of the organsims name

Question 17

What is the organism

Answer 17

the formal scientific name for the source organism

Question 18

What does direct submission mean

Answer 18

the person who added the sequence and the date that the sequence was added to the database

Question 19

What does CDS mean

Answer 19

coding sequence

Question 20

What is an exon

Answer 20

definitive region of genome that codes for a portion of spliced mRNA, rRNA, or tRNA, may contain 5’UTR, all CDSs and 3’UTR

Question 21

What is an intron

Answer 21

a segment of DNA that is transcribed but removed from within the transcript by splicing together the sequences on either side of it

Question 22

What is a gene

Answer 22

a region of biological interest identified as a gene and for which a name has been assigned

Question 23

What is a location

Answer 23

a site between two adjoining nucleotides such as a restriction enzyme site that is indicated by listing the two points separated by ^

Question 24

What is a sequence span

Answer 24

indicated using the starting base number and the ending base number separated by two periods

</> symbols may be used with the starting and ending numbers to indicate that an end point is beyond the specified base numbers

Question 25

What is a location operator

Answer 25

a prefix that specifies what must be done to the indicated sequence to find or construct the location corresponding to the feature

Question 26

What are common operators

Answer 26

complement
join

Question 27

What is complement

Answer 27

find the complement of the sequence and then present it in 5’ to 3’

Question 28

What is join

Answer 28

the indicated elements should be joined to form one contiguous sequence

Question 29

What is complment join

Answer 29

the indicated elements should be joined to form a contiguous sequence and then take the complement and place it in 5’ to 3’ orientation