Genomics: analysis and algorithms. Multiple alignment

Multiple alignment of DNA

Create multiple alignemts, try three different programs clustalw, clustalo a muscle. Programs are installes on VM, all are easy to install or you can use online version availabkle at EBI. For visualization you can uyse clustalx or mview, both available online at EBI.

Data:

• cyc.fasta
• gss.fasta

Biology

Create multiple alignment of HIV proteins gp120. Use biological knowledge to confirm, that your alignment is valid

gp120 contains 9 conserved disulfide bridges. Also relevant is the so-called V3-loop. This is a surface-exposed highly immunogenic antibody-binding and hypervariable (immunological escape) region of gp120, which has been extensively sequenced.

• gp120
• schema

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The Rox1 transcription factor is known to bind at least eight sites in three genes in the Saccharomyces cerevisiae genome. Compute:

• Position Count Matrix
• Position Probability Matrix
• Position Frequency Matrix
• Consensus sequence
• Logo

    HEM13 CCCATTGTTCTC
    HEM13 TTTCTGGTTCTC
    HEM13 TCAATTGTTTAG
    ANB1  CTCATTGTTGTC
    ANB1  TCCATTGTTCTC
    ANB1  CCTATTGTTCTC
    ANB1  TCCATTGTTCGT
    ROX1  CCAATTGTTTTG