SlideShare a Scribd company logo
How  to  use  Tutorial
Benchmark	
  &	
  Predic/on	
  tools	
  for	
  miRNAs	
  iden/fica/on	
  
www.integra/vebioinforma/cs.me/mirquest	
  
Ø Trough	
  this	
  tutorial	
  you	
  will	
  learn	
  how	
  to:	
  
Ø 	
  Perform	
  benchmark	
  between	
  the	
  currently	
  available	
  miRNA	
  predic/on	
  tools	
  
in	
  order	
  to	
  choose	
  the	
  best	
  one	
  to	
  work	
  with	
  your	
  organims;	
  
Ø 	
  Iden/fy	
  miRNAs	
  using	
  your	
  own	
  datasets.	
  
Ø The	
  first	
  step	
  is	
  to	
  go	
  to	
  the	
  TOOL	
  tab,	
  marked	
  with	
  the	
  yellow	
  arrow.	
  	
  
Ø Once	
  there,	
  you	
  should	
  see	
  the	
  currently	
  available	
  tools	
  for	
  the	
  microRNAs	
  predic/on.	
  	
  
Ø It	
  is	
  possible	
  to	
  select	
  one	
  or	
  more	
  tools.	
  
Ø AJer	
   you	
   choose	
   one	
   or	
   more	
   of	
   them,	
   you	
   will	
   be	
   able	
   to	
   set	
   (if	
   needed)	
   	
   different	
  
parameters.	
  Default	
  values	
  are	
  shown.	
  
Ø AJer	
   define	
   the	
   soJware	
   parameters,	
   you	
   need	
   to	
   choose	
   between	
   the	
   two	
   main	
  
func/onali/es	
  of	
  miRQuest:	
  Benchmark	
  or	
  Iden,fica,on	
  	
  
Ø 	
  If	
  you	
  choose	
  to	
  perform	
  a	
  Benchmark	
  analysis,	
  It	
  is	
  necessary	
  provide	
  e-­‐mail	
  to	
  receive	
  the	
  
results	
  and	
  defined	
  the	
  two	
  dataset	
  file	
  (posi/ve	
  and	
  nega/ve)	
  in	
  FASTA	
  format.	
  
Ø You	
  can	
  see	
  below	
  the	
  examples	
  about	
  the	
  two	
  files.	
  Note	
  that	
  there	
  are	
  some	
  exemplary	
  
files	
  available	
  to	
  download:	
  
	
  
Ø Posi%ve	
  file:	
  Mul/	
  FASTA	
  file	
  containing	
  proved	
  miRNA	
  sequences.	
  It	
  must	
  have	
  FASTA,	
  FA	
  or	
  TXT	
  extension	
  
and	
  it	
  cannot	
  be	
  larger	
  than	
  5	
  mb.	
  For	
  example:	
  
	
  
	
  
	
  
	
  
Ø Nega%ve	
  file:	
  Mul/	
  FASTA	
  file	
  containing	
  non	
  miRNA	
  sequences	
  (i.e.	
  mRNA	
  sequences).	
  It	
  must	
  have	
  FASTA,	
  
FA	
  or	
  TXT	
  extension	
  and	
  it	
  cannot	
  be	
  larger	
  than	
  5	
  mb.	
  For	
  example:	
  
Ø Finally,	
  clicking	
  Process	
  will	
  trigger	
  the	
  benchmark	
  calcula/on.	
  You	
  should	
  receive	
  an	
  email	
  
with	
  the	
  graphs	
  &	
  sta/s/cs	
  among	
  the	
  different	
  selected	
  soJwares.	
  
Ø On	
  the	
  other	
  hand,	
  if	
  you	
  choose	
  to	
  perform	
  a	
  Iden,fica,on	
  analysis,	
  you	
  only	
  need	
  to	
  point	
  
out	
  your	
  e-­‐mail	
  and	
  the	
  mul/	
  FASTA	
  file	
  with	
  the	
  sequences	
  to	
  be	
  analyzed.	
  
How  to  Tutorial
Benchmark	
  &	
  Predic/on	
  tools	
  for	
  miRNAs	
  predic/ons	
  	
  
www.integra/vebioinforma/cs.me/mirquest	
  

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miRQuest - How to use Tutorial

  • 1. How  to  use  Tutorial Benchmark  &  Predic/on  tools  for  miRNAs  iden/fica/on   www.integra/vebioinforma/cs.me/mirquest  
  • 2. Ø Trough  this  tutorial  you  will  learn  how  to:   Ø   Perform  benchmark  between  the  currently  available  miRNA  predic/on  tools   in  order  to  choose  the  best  one  to  work  with  your  organims;   Ø   Iden/fy  miRNAs  using  your  own  datasets.  
  • 3. Ø The  first  step  is  to  go  to  the  TOOL  tab,  marked  with  the  yellow  arrow.    
  • 4. Ø Once  there,  you  should  see  the  currently  available  tools  for  the  microRNAs  predic/on.     Ø It  is  possible  to  select  one  or  more  tools.  
  • 5. Ø AJer   you   choose   one   or   more   of   them,   you   will   be   able   to   set   (if   needed)     different   parameters.  Default  values  are  shown.  
  • 6. Ø AJer   define   the   soJware   parameters,   you   need   to   choose   between   the   two   main   func/onali/es  of  miRQuest:  Benchmark  or  Iden,fica,on    
  • 7. Ø   If  you  choose  to  perform  a  Benchmark  analysis,  It  is  necessary  provide  e-­‐mail  to  receive  the   results  and  defined  the  two  dataset  file  (posi/ve  and  nega/ve)  in  FASTA  format.  
  • 8. Ø You  can  see  below  the  examples  about  the  two  files.  Note  that  there  are  some  exemplary   files  available  to  download:     Ø Posi%ve  file:  Mul/  FASTA  file  containing  proved  miRNA  sequences.  It  must  have  FASTA,  FA  or  TXT  extension   and  it  cannot  be  larger  than  5  mb.  For  example:           Ø Nega%ve  file:  Mul/  FASTA  file  containing  non  miRNA  sequences  (i.e.  mRNA  sequences).  It  must  have  FASTA,   FA  or  TXT  extension  and  it  cannot  be  larger  than  5  mb.  For  example:  
  • 9. Ø Finally,  clicking  Process  will  trigger  the  benchmark  calcula/on.  You  should  receive  an  email   with  the  graphs  &  sta/s/cs  among  the  different  selected  soJwares.  
  • 10. Ø On  the  other  hand,  if  you  choose  to  perform  a  Iden,fica,on  analysis,  you  only  need  to  point   out  your  e-­‐mail  and  the  mul/  FASTA  file  with  the  sequences  to  be  analyzed.  
  • 11. How  to  Tutorial Benchmark  &  Predic/on  tools  for  miRNAs  predic/ons     www.integra/vebioinforma/cs.me/mirquest