1a) Which software system can produce e a) b) SAMtools c) BEDtools 19) What is ChiP. seq designed to measure? a) mRNA expression levels b) The 3D physical location of two pieces of c) The location of nucleosomes d) The location where proteins bind to DNA 20) used to identify epigenetic modifiers such as a) Enzymes b) Transoription factors c) INDELs d) SNVs Part Il. (20 pts) True/False. I nefaise, if the statement is false, correct in the simplest way to make the statement u Sisss is a tool used to identify protein binding sites on DNA sequences. are often implemented in MSA in order to vary lengths of the sequences being aligned then pairwise sequence most similar to the rest of the sequences in the center alignments are performed with the rest of the sequences. 3. Multiple sequence alignment uses the star alignment houristic algorithm by setting the 4. Sequence alignment can help identify conservation in proteins across species and The Basic Local Alignment Search Tool uses its own heuristic algorithm and is a popular tool for aligning nucleotide or protein sequences 6. Single end sequencing is essential for RNA-seq 7. A BAI file is used to view BAM files 5. Gene isoforms are mRNAs produced from the same locus but differ in transcription sta sites (TSSs), protein coding DNA sequences (CDSs) and/or untranslated regions (UTRs), potentially altering gene function. 8. Splice junctions are the intron/intron junctions, at which splicing takes place