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. 5 S T A T I S T I C A L A N A LY S I S O F A L I G N M E N T S in .NET Integrating qr barcode in .NET . 5 S T A T I S T I C A L A N A LY S I S O F A L I G N M E N T S




How to generate, print barcode using .NET, Java sdk library control with example project source code free download:
3 . 5 S T A T I S T I C A L A N A LY S I S O F A L I G N M E N T S use none none printing tointegrate none in none Java human I G G S none none K P R V A T P E V V S K I A Q Y K R E C P S I F A W E I R D R L L S E G V C T N D N I P S V S S I N R V L R N L A S E K - Q Q. human H S G V N Q L G G V F V N G R P L P D S T R Q K I V E L A H S G A R P C D I S R I L Q V S N G C V S K I L G R Y Y E T G S I R P R A. Example 3.2 S none for none igni cance of global alignment. Remember that for the global alignment:.

A(s, t) = V V I I V V A A L D A A S V V E G A I S S,. we have a sco none for none re of 2, resulting from seven matches, two mismatches, and three gaps (using our elementary scoring scheme). Now, if we do 1000 random permutations of the second sequence, t, and we nd the best global alignment for it with s for every randomization, we get the distribution of alignment scores observed in Figure 3.1.

Only twice out of the 1000 permutations did we nd an alignment score equal to or greater than the observed score (in fact, we never see a higher score). This can be interpreted as a p-value of 0.002.

We must conclude that our original alignment is highly signi cant, and would arise by chance much less than 1% of the time. We can also do the same type of permutation test for local alignments, with little difference in interpretation, as seen in the following example..

Local alignme nt of PAX genes. We have seen that the eyeless protein is one of many factors controlling the development of eyes in many distantly related species. Like eyeless, many other PAX and HOX genes are expressed in the developing nervous system and are believed to help regulate neurogenesis.

We demonstrate how to use local and global alignment algorithms by discovering conserved domains in PAX and HOX proteins, nding the celebrated paired-box and homeobox domains. This can readily done by rst downloading two sequences from GenBank, one from human and the other from fruit y, corresponding to the coding regions of the PAX gene discussed in the opening story. Since eukaryotic genes often contain introns, we can get a le from GenBank that contains the sequence of just the mRNA (and the associated protein), where introns have already been removed.

The accession numbers are AY707088 and NM 001014694. We expect these genes to contain two segments in common: a longer segment the PAX domain and a shorter segment the HOX domain. By running Smith Waterman local alignment, we obtain the segment of 133 amino acids shown in the adjacent table The score of this alignment (437, with a PAM 50 substitution matrix) is then tested against the score of 1000 alignments between randomized sequences, and is never equaled, indicating a highly signi cant result (see histogram in Figure 3.

2). Indeed, this sequence is found to correspond to the PAX domain, and is in the very beginning of these two sequences (within the rst 200 amino acids)..

HSGVNQLGGVFVGGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRA More sophisti cated methods are available, based on a theoretical analysis of the distribution of scores for random sequences, but they are too complicated for the purpose of this introductory book. Pointers to literature about advanced methods can be found in Section 3.10.

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