Friday, June 5, 2020

Bioinformatics Gap Penalty, Genomic Alignment - 1100 Words

Bioinformatics: Gap Penalty, Genomic Alignment, Pairwise Sequence (Math Problem Sample) Content: SurnameCourseTutorInstitutionDateQUESTION 1 (PAIRWISE ALIGNMENT) 1 Types of pairwise sequence alignments are; * Global alignment this creates an end to end alignment of the sequence to be aligned. * Genomic alignment this emphasizes on DNA alignment while accounting for characteristics present in the genomic data. * Local alignment this one finds one or more alignments describing the most similar regions within the sequence to be aligned. 2 Linear gap penalty, is a gap penalty in which each inserted/deleted symbol in the gap contributes a constant negative score to the alignment, while affine gap penalty penalizes using insertion and deletion using a linear function in which one term is length independent. So, affine gap penalty combines both constant and linear gap penalties, that is why is the most preferable. 3 Gap penalty 2, Match +3 and Mismatch 1.Step 1; we draw the (n+1) X (m+1) grid and populate the values CGGACAGT, CGAC. We will put a gap in the first box of the matrix, as follows:T G A C A G G C C G A C Step 2; We fill in the table with the first value being a gap (0). Then we add the numbers starting from zero to the gap value. E.g. 0 +(-2)= - 2, -2+(-2)=-4 and so on.T -16 G -14 A -12 C -10 A -8 G -6 G -4 C -2 0 -2 -4 -6 -8 C G A C Step 3: We fill in the rest of the table by adding; the box beside (+gap), the box at the bottom(+gap) and the diagonal box with the match and mismatch parameters. The we identify which one brings the higher score and indicate by an arrow which one brought the higher score, thats what we indicate as follows;T -16 -692151670050017 11112517272000-154305-50800019 13843015875000-167640-63500021 14478016192500-15303512700023 G -14 -647701746250015 9461516002000-163830-50800017 -100330-50800019 16827517589500-90805-50800021 A -12 -749301593850013 193040-69850011493519177000-158115-152400015 10541017716500136525-298450017 -1 047756350019 C -10 -717551555750011 10160017589500-130175-50800013 10922015748000-97790-63500015 167640-234950016129016446500-13398569850017 A -8 -67310149860009 10096516065500-130175-127000011 -117475-50800013 -124460-50800015 G -6 7 8445516192500-17399019050009 1098551892300099695-2984500-1041406350011 14668516637000151765-2730500-126365-25400013 G -4 -60960-3556000-61595158750005 -163830-5715007 -117475-8890009 -12890519050011 C 17589520129500-2 3 -163195-8255001 -166370-1206500-1 -1581153810000-17018019177000-3 0 -2 -4 -6 -8 C G A C Step 4; We want to make a trace back. Here, we need to find the highest value, usually the highest value is always at the last corner of the matrix. Ours is +23 (most suitable value). We trace it back to the starting point 0. So we require the arrows to know from which the value comes from until we get to 0. In our box, we will use a shading of red to show the traceback.T -16 -692151670050017 11112517272000-154305-50800019 13843015875000-167640-63 500021 14478016192500-15303512700023 G -14 -647701746250015 9461516002000-163830-50800017 -100330-50800019 16827517589500-90805-50800021 A -12 -749301593850013 193040-69850011493519177000-158115-152400015 10541017716500136525-298450017 -1047756350019 C -10 -717551555750011 10160017589500-130175-50800013 10922015748000-97790-63500015 167640-234950016129016446500-13398569850017 A -8 -67310149860009 10096516065500-130175-127000011 -117475-50800013 -124460-50800015 G -6 7 8445516192500-17399019050009 1098551892300099695-2984500-1041406350011 14668516637000151765-2730500-126365-25400013 G -4 -60960-3556000-61595158750005 -163830-5715007 -117475-8890009 -12890519050011 C 17589520129500-2 3 -163195-8255001 -166370-1206500-1 -1581153810000-17018019177000-3 0 -2 -4 -6 -8 C G A C orT -16 -692151670050017 11112517272000-154305-50800019 13843015875000-167640-63500021 14478016192500-15303512700023 G -14 -647701746250015 9461516002000-163830-50800017 -100330-50800019 16827517589500-90805-50800 021 A -12 -749301593850013 193040-69850011493519177000-158115-152400015 10541017716500136525-298450017 -1047756350019 C -10 -717551555750011 10160017589500-130175-50800013 10922015748000-97790-63500015 167640-234950016129016446500-13398569850017 A -8 -67310149860009 10096516065500-130175-127000011 -117475-50800013 -124460-50800015 G -6 7 8445516192500-17399019050009 1098551892300099695-2984500-1041406350011 14668516637000151765-2730500-126365-25400013 G -4 -60960-3556000-61595158750005 -163830-5715007 -117475-8890009 -12890519050011 C 17589520129500-2 3 -163195-8255001 -166370-1206500-1 -1581153810000-17018019177000-3 0 -2 -4 -6 -8 C G A C 4 A local alignment on the sequences, we look for the trace back path (places shaded red)...