Pairwise alignment of the DNA sequence using hypercomplex number representation.
نویسندگان
چکیده
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex number representation of the DNA base-nucleic acid codes and incorporated with the method of dot matrix analysis and various algorithms of sequence alignment. The problem of DNA sequence alignment can be processed in a rather similar way to pairwise alignment of the protein sequence.
منابع مشابه
Hypercomplex cross-correlation of DNA sequences
A hypercomplex representation of DNA is proposed to facilitate comparing DNA sequences with fuzzy composition. With the hypercomplex number representation, the conventional sequence analysis method, such as, dot matrix analysis, dynamic programming, and cross-correlation method have been extended and improved to align DNA sequences with fuzzy composition. The hypercomplex dot matrix analysis ca...
متن کاملgpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences
Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...
متن کاملEvolutionary Two-Dimensional DNA Sequence Alignment
This article presents a model for DNA sequence alignment. In our model, a finite state automaton writes two-dimensional maps of nucleotide sequences. An evolutionary method for sequence alignment from this representation is proposed. We use HIV as the working example. Experimental results indicate that structural similarities produced by two-dimensional representation of sequences allow us to p...
متن کاملMultiple Sequence Alignment Using Three- Dimensional Fragments
Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of us...
متن کاملAn Application of the ABS LX Algorithm to Multiple Sequence Alignment
We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit for the length of the sequences. Our goal here is to ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bulletin of mathematical biology
دوره 66 5 شماره
صفحات -
تاریخ انتشار 2004