BIOL/CMPU 353 - Bioinformatics
Smith and Schwarz
Spring 2012

Assigned: Tue, Feb 28
Due: Tue, Mar 20 (after spring break)

We just spent a field trip at CSHL learning about the role of 3’UTRs in regulating gene expression and bioinformatic approaches for identifying genes whose 3’UTRs are targeted by miRNAs. Now let’s think about the role of 5’UTRs. These regions of the mRNA are likely involved in regulating gene expression and translation, but little is known about how these function. Let’s say that we are interested in isolating the 5’UTR regions from a transcriptome, so that we can study them. How might we design an approach for identifying them? We can use blast searches to help us.

Imagine you’ve just Blasted your large set of sequences against an even larger database, and after many hours (or days) running on your high-performance parallel computing cluster, you have a still larger Blast results file! What now?

• Blast search previously executed. File located at
  /home/joschwarz/public/AiptasiaTranscriptome_v_SwissProt.blastx
  
  • This is the file that your program should read from
  • Please do NOT copy this file due to its large size (almost 0.6 GB)

• Background needed
  • PEDNA Ch 8: Reading text files (fasta, blast results, any text file)
  • Finite State Machines: a framework for designing parsing algorithms

• Starter code: assign3v1.pl.txt
  • modify this code to read Jodi’s blast results file
  • add additional states and state transitions
  • remember: we want to print only those hits whose alignments begin with an M, and the M occurs in the first position of the Subject: sequence.

• Output format notes:
  • columns should be tab-delimited to make importing into a spreadsheet easier
  • our algorithm found 4341 4370 1) predicted 5’ UTRs—too many to reasonably list!
  • here are the first 15 predictions from our output

    EST	EST Length	Query Start Position
    Locus_89379_Transcript_1	3623	2244
    Locus_82449_Transcript_1	3961	421
    Locus_82448_Transcript_1	4162	421
    Locus_82446_Transcript_1	3999	407
    Locus_97156_Transcript_1	4598	4489
    Locus_21618_Transcript_1	1175	29
    Locus_124359_Transcript_1	2118	659
    Locus_125402_Transcript_3	1999	92
    Locus_125403_Transcript_1	1880	92
    Locus_129236_Transcript_1	5316	73
    Locus_129235_Transcript_1	5557	73
    Locus_129234_Transcript_1	5212	73
    Locus_52816_Transcript_1	2177	1123
    Locus_52819_Transcript_1	1860	759
    Locus_52818_Transcript_1	1212	164