L4 - Bioinformatics 1

Question 1

what are bioinformatics

Answer 1

bridges the gap between BIG daya sets ajnd actual biological understanding

Question 2

overview of bioninformatixs proscess

Answer 2

have a query/question

probe database

evaluate results

Question 3

2 types of nucleotide databases

Answer 3

primary:
experimental data depoisioted direcetly by scientists
= GenBank

secondly:
info from a primary database but processed
= RefSeq

Question 4

name a primary and secondary database

Answer 4

Genbank:
interbational database from EMBL,NCBI and Japan.
can have multiple copies of the same nucleotide sequnce each with a ‘UNIQUE’ accession number

RefSeq:
manually curated database from GenBank

Question 5

what is UniProtKB comprised of

Answer 5

TreEMBL:
protein sequences automatically annotated by computer from nucletide sequnces = unrevewed and redundant

Swiss-Prot:
manual,high quality annotatuion,reviewed, non-redundant gold standard.

non-redundant = 1 record per molecule per species for fully sequnced organisms

Question 6

what else does Uniprot do

Answer 6

cross-referebce and link to other resources

useful entry point to start investigating a protein

Question 7

what is FASTA format

Answer 7

displays both DNA and protein sequnces without spaces

commonly usedf for analysis programmes

Question 8

the linking of sequnce , structure and function

Answer 8

amino acid sequnce determines the structure which in turn dictates a proteins function

Homologous proteins share conserved amino acid patterns adopting similar folds with related functions

= we can use this to predict the function of a protein if we know its amino acid sequnce

Question 9

what are protein domains

Answer 9

structural units of abount 50 amino acids

proteins can contain multiple domains

Question 10

what is InterproScan

Answer 10

comapres query sequence to all other sequnces

assigns probability for any amino acid at a particular position within a domain whether they are identical or non-conserved

a threshold score determines if a certain domain is likely to be present

= InterproScan does all this and tells you which part of your protein is likely to have which domains

Question 11

what is Prosite

Answer 11

identifies post-translational modifications

finds patterns using short mtofs linked ton modifications

generates hypothesis about your protein that you can then go and test