Tools Exam Questions

   

One aspect of bioinformatics concerns algorithms: computational tools that allow us to analyse the data and support our inferences.

   

2003

WWW servers for the multiple alignment program T-Coffee require only a set of sequences as input for their task. Obviously, the important parameters the program uses are hidden - they have been set to a reasonable default.

Briefly discuss the key parameters that such a program needs and how they influence the result.

2003

" Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devastating threats to food security worldwide. Conservatively, each year enough rice is destroyed by rice blast disease to feed 60 million people [...]. Indeed, the Centers for Disease Control and Prevention has recently recognized and listed rice blast as a significant biological weapon. No part of the world is now safe from this disease. It was long thought of as being confined to developing nations, but over the past decade it has emerged as a serious problem in the United States. [...] Widespread devastation of golf courses, particularly in the Midwest, where it has been attacking cool season grasses, is of particular concern. "

[... excerpt from the Web pages of the US Magnaporthe grisea genome project of the Center for Genome Research]

 

In an effort to annotate the M. grisea genome, you have done a BLAST search of the E. coli Glutaminyl tRNA synthetase gene against the predicted M. grisea open reading frames: your goal is to find the orthologue of this gene. You have chosen the "nr" database and have limited the search output to magnaporthe grisea"[organism] in the appropriate advanced-options field of the Web form. Here are excerpts from the output you receive:  

Sequences producing significant alignments:                      (bits) Value

gi|38104873|gb|EAA51376.1|  hypothetical protein MG09393.4 [...   391   e-109 
gi|38106536|gb|EAA52828.1|  hypothetical protein MG05956.4 [...   268   3e-72 
gi|38106250|gb|EAA52583.1|  hypothetical protein MG05275.4 [...    59   2e-09 
gi|38101579|gb|EAA48524.1|  hypothetical protein MG00182.4 [...    30   1.7
  

Comment briefly on each of the portions of the above excerpt from the BLAST output, that is formatted in bold and red.

>gi|38106250|gb|EAA52583.1| hypothetical protein MG05275.4 [Magnaporthe grisea ]
          Length = 594

 Score = 59.3 bits (142), Expect = 2e-09
 Identities = 61/243 (25%), Positives = 102/243 (41%), Gaps = 34/243 (13%)

Query: 30  TRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPVKEDIEYVESIKNDVEWL 89
           TRF P P G+LH+G  ++   N+ +A+   GQ  LR +DT+  +   +    +  D+ W 
Sbjct: 61  TRFAPSPTGFLHLGSLRTALFNYLLAKATGGQFLLRLEDTDRTRIVPDAEARLYQDLRWA 120

Query: 90  GFHW---------SGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPEQIREYR-GTLTQ 139
           G  W         SG  R  S+       YA +L++ G AY    T E++   + G+   
Sbjct: 121 GLVWDEGPDVGGPSGPYR-QSERLGHYSKYAQQLLDSGRAYRCFCTREELAASQLGSQAD 179

Query: 140 PGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEH 199
            G    Y    +  +    E+  A G       +R + +  +PF V   P L   +F + 
Sbjct: 180 SGAGGRYPGTCLAVSADESEERAARG---DAHVIRFRSN-TTPFTV---PDLVYRRFRKK 232

Query: 200 HQTGN----KWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPR 255
           H   +    K   +P Y F + + D L  +TH +         R  +W+   I+ P+H  
Sbjct: 233 HMEDDFIIMKSDGFPTYHFANVVDDHLMDVTHVI---------RGAEWL---ISTPMHCD 280

Query: 256 QYE 258
            Y+
Sbjct: 281 LYD 283
   

• Briefly discuss what you can conclude about MG05275.4 from the above excerpt of the BLAST report.
• Describe at least two approaches for functional annotation that are not based on homology that you can use to annotate MG05275.4 ?
• Would the same search using PSI-BLAST rather than BLAST have helped for your task?

2002

File:Stereo 000000.jpg

Caption.

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