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why is gap opening penalized more than gap extension in doing alignment of sequence similarity?
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- Why a multiple sequence alignment is needed for researchers? What inferences can be derived from this kind of sequence alignments? Explain two extreme cases that are non-informative for the multiple sequence alignment.What are the similarities and/or differences between interpreting Multiple Sequence Alignment (MSA) of conserved sequences at the DNA level versus the Amino Acid level? Please site references if possible and have 5+ sentences.What is meant by the term "alignment" in genomic research and in what ways does alignment aid sequence assembly? How can relying on alignment lead to potential errors?
- if i had 3 sequences that were 15 nucleotides long. how would i make an optimal sequence alignment using gaps?In reversible terminator sequencing, how would the sequencing process be affected if the 3′-end-blocking group of each nucleotide were replaced with the 3′-H present in the dideoxynucleotides used in Sanger sequencing?Why is sequence alignment critical to phylogenetic analysis?
- If you have access to the necessary computer software, make asequence file and analyze it in the following ways: What is thetranslated sequence in all three reading frames? What is the longest open reading frame? Is the sequence homologous to any known sequences? If so, does this provide any clues about the function of the sequence?what is the minimum edit distance between the following pair of sequences? TTGACG TTTAGT - 0 - 1 - 2 - 3How are the gap penalties adjusted in the ClustalW multiple sequence alignment program to improve the algorithm? Indicate the logic only.