Test yourself: 1

EU name: EXINT1

 (Date: Aug 24 2016 EXINT1 )

This page contains a randomly selected series of exam questions that we have used in the past in real exams, and that you should be able to answer by now.

You find all these questions again in the ′Test-exams′ section, and in that section, you often also find the answers.

Exam questions used in the past:

  1. A colleague has sequenced a novel gene. He comes to you and asks for help. What do you do first and why?
  2. What are the major strengths and the major weaknesses of the SwissProt database?
  3. What is the role of the accession code in sequence databases?
  4. What are the major advantages and disadvantages of WWW based servers?
  5. What is the difference between a SNP and a mutation mentioned in OMIM?
  6. What are BLAST and MRS abbreviations of, and what kind of searches can be done with these two programs?
  7. What is a Dayhoff matrix?
  8. If a match from a BLAST database search is reported to have an E-value of 0.0, should it be considered highly insignificant or highly significant?
  9. What is the role of the accession-code in databases?
  10. Give 4 examples of protein features that can be found in the feature section of a SwissProt file.
  11. Sequence alignment is an important tool? Write down three scientifically relevant biological questions that can be answered with/using sequence alignment(s). (So, don't ask trivial things like "What does the alignment look of...").
  12. In January 2009, I ran BLAST on a bacterial protease against SwissProt. I found a hit. In August 2012, I did the same run, and got the same hit, but this time the E-score of this same hit was worse than in January. Why?
  13. Below you see a part of a BLAST output. Explain: Query
    Subject
    The occurrence of the region with the XXXXX
    How to circumvent XXXX in the output
    The --
    The ... 

Query: 361 ILNPYIINVTLAAKMCSQVLCQEQGVCIRKNWNSSDYLHLNPDNFAIQLEKGGKFTVRGK 420
           ILNPYI.NV LAA.MCSQVLCQ.QGVCIRKNWNS...LHLNPDNFAI     GK.TVRGK
Sbjct: 361 ILNPYILNVALAARMCSQVLCQQQGVCIRKNWNSTNFLHLNPDNFAILS--RGKYTVRGK 418
 
Query: 421 PTLEDLEQFSEKFYCSCYSTLSCKEXXXXXXXXXXXXCIADGVCIDAFLKPPMETEEPQI 480
           PTLED.EQF.EKF.CSCY TLSCKE            CIADGVCIDA.LKP METEEPQI
Sbjct: 418 PTLEDIEQFTEKFFCSCYGTLSCKEKADVADVDAVDVCIADGVCIDAYLKPTMETEEPEI 478 *END

Another question that often comes back is to tell me what A-K are in this BLAST output figure.