Homework 3: Fill in the blank – 3 points each – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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You are given the complete genomic sequence of Escherichia coli O157:H7 str. Sakai plasmid pO157, NCBI Reference Sequence: NC_002128.1, in a file named sequence.fasta that can be opened as a text file in Word or another text editor program. Use this sequence to perform the following:
- Use fgenesB from Softberry for bacterial operon and gene prediction
- Use BPROM from Softberry for prediction of bacterial promoters
- Use FindTerm from Softberry for finding terminators in bacterial genomes
- Use ORF-Finder ignoring nested ORFs for gene prediction
From the fgenesB results, how many genes were predicted from this sequence?
From the fgenesB results, how many transcription units were predicted from this sequence?
From the fgenesB results, how many operons were predicted from this sequence?
From the BPROM results, how many promoters were predicted from this sequence?
From the FindTerm results, what is the best terminator score for the sequence?
From the FindTerm results, what is the length of the best terminator in base pairs?
From the ORF-Finder results, how many ORFs were found from this sequence?
Find the complete genome for the Zika virus in NCBI (NCBI Reference Sequence: NC_012532). Use this sequence to perform the following:
- Use fgenesV from Softberry for viral gene prediction
- Use fgenesV0 from Softberry for viral gene prediction
From the fgenesV results, how many genes were predicted from this sequence?
From the fgenesV0 results, how many genes were predicted from this sequence?
Compare results between different algorithms, for example fgenesV, fgenesV0, and ORF-Finder (done previously) for the Zika virus and fgenesB and ORF-Finder for Escherichia coli. Do you notice variation between results? Type out your answer but do not provide further explanation here (e.g., Yes/No).
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