SAM: String-based sequence search algorithm for mitochondrial DNA database queries

Fast Semi-local Alignment for DNA Sequence Database Search

Given a query DNA sequence, our goal is to find in the DNA sequence database all the sequence segments that are similar to the query. In this paper we present a stringto-signal transform technique that can transform a DNA sequence into a four-channel signal. Without considering gaps, the edit distance between two DNA sequences can be calculated as the sum of absolute difference (SAD) between th...

Mitochondrial DNA sequence-based phylogenetic relationship of Trichiurus lepturus (Perciformes: Trichiuridae) from the Persian Gulf

In this study, mitochondrial DNA analysis using 16S ribosomal DNA (rDNA) was performed to investigate the phylogeny relationship of Trichiurus lepturus in the Persian Gulf compared to the other investigated area. The amplification of 16S rDNA resulted in a product of 600 bp in all samples. The results showed that the isolated strain belongs to T. lepturus showing 42 divergence sites among the s...

An Edit Distance based algorithm for String / Sequence Classification

An improved opposition-based Crow Search Algorithm for Data Clustering

Data clustering is an ideal way of working with a huge amount of data and looking for a structure in the dataset. In other words, clustering is the classification of the same data; the similarity among the data in a cluster is maximum and the similarity among the data in the different clusters is minimal. The innovation of this paper is a clustering method based on the Crow Search Algorithm (CS...

Polyphonic Musical Sequence Alignment for Database Search

Finding the best matching database target to a melodic query has been of great interest in the music IR world. The string alignment paradigm works well for this task when comparing a monophonic query to a database of monophonic pieces. However, most tonal music is polyphonic, with multiple concurrent musical lines. Such pieces are not adequately represented as strings. Moreover, users often rep...