Combinatorial pattern matching algorithms in computational by Gabriel Valiente

By Gabriel Valiente

Emphasizing the hunt for styles inside of and among organic sequences, timber, and graphs, Combinatorial development Matching Algorithms in Computational Biology utilizing Perl and R exhibits how combinatorial development matching algorithms can remedy computational biology difficulties that come up within the research of genomic, transcriptomic, proteomic, metabolomic, and interactomic information. It implements the algorithms in Perl and R, accepted scripting languages in computational biology.

The e-book presents a well-rounded rationalization of conventional matters in addition to an updated account of more moderen advancements, akin to graph similarity and seek. it truly is equipped round the particular algorithmic difficulties that come up while facing constructions which are mostly present in computational biology, together with organic sequences, bushes, and graphs. for every of those buildings, the writer makes a transparent contrast among difficulties that come up within the research of 1 constitution and within the comparative research of 2 or extra constructions. He additionally provides phylogenetic timber and networks as examples of bushes and graphs in computational biology.

This e-book offers a complete view of the full box of combinatorial development matching from a computational biology viewpoint. besides thorough discussions of every organic challenge, it comprises designated algorithmic ideas in pseudo-code, complete Perl and R implementation, and tips that could different software program, akin to these on CPAN and CRAN.

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Example text

The phosphates form covalent bonds between the 3 carbon of one sugar and the 5 carbon of the next sugar along the backbone, thus defining a direction of the DNA sequence from the unbound 5 carbon to the unbound 3 carbon. In vivo, DNA consists of two strands held together by hydrogen bonds between complementary nucleotides, which fold in space in the shape of a double helix. Adenine and thymine are complementary, and the AT base pair has two hydrogen bonds. Guanine and cytosine are also complementary, and the GC base pair has three hydrogen bonds instead.

Given the k-mer composition of two biological sequences, their alignment free distance can be obtained by computing the linear correlation coefficient of the k-mer frequencies, that is, by dividing the covariance of the k-mer frequencies by the product of their standard deviations. function alignment free distance(S1 , S2 , k, Σ) F1 ← word composition(S1 , k, Σ) F2 ← word composition(S2 , k, Σ) cov ← covariance(F1 , F2 ) sd1 ← standard deviation(F1 ) sd2 ← standard deviation(F2 ) return cov/(sd1 sd2 ) The representation of sequences in BioPerl does not include any method to compute the linear correlation coefficient of the k-mer frequencies of two sequences.

Use Bio :: DB :: GenBank ; my $db = Bio :: DB :: GenBank - > new ; my $seq = $db - > get_Seq_by_gi ( " 48994873 " ) ; The representation of sequences in BioPerl includes additional methods for performing various operations on sequences; for instance, to access the identifier of a sequence, my $id = $seq - > id ; to obtain the length of a sequence, my $len = $seq - > length ; © 2009 by Taylor & Francis Group, LLC 40 Combinatorial Pattern Matching Algorithms in Computational Biology to get the accession number or unique biological identifier for a sequence, my $acc = $seq - > accession_number ; to access the description of a sequence, my $desc = $seq - > desc ; to obtain the subsequence of a DNA, RNA, or protein sequence contained between an initial and a final position, as a character string, use Bio :: Seq ; my $s = " G G G U G C U C A G U A C G A G A G G A A C C G C A C C C " ; my $seq = Bio :: Seq - > new ( - seq = > $s ) ; my $prefix = $seq - > subseq (1 ,12) ; my $suffix = $seq - > subseq (9 , $seq - > length ) ; to truncate a DNA, RNA, or protein sequence from an initial to a final position into a sequence instead of just a character string, my $s = " S C F A L I S G T A N Q V K C Y R F R V K K N H R H R Y E N C T T T W F T V A D N G A E RQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF "; my $seq = Bio :: Seq - > new ( - seq = > $s ) ; my $t = $seq - > trunc (4 ,9) ; and to obtain the reverse complement of a DNA or RNA sequence.

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