This paper announces an algorithm for finding pattern similarities between two given finite sequences. Two portions, one from each sequence, are similar if they are close in the metric space of evolutionary distances. In its most general form the algorithm allows a complete list to be made of all pairs of intervals, one from each of the two given sequences, such that each pair displays a maximu...

A method of finding pattern similarities between two sequences is given. Two portions, one from each sequence, are similar if they are close in the metric space of evolutionary distances. The method allows a complete list to be made of all pairs of intervals, one from each of two given sequences, such that each pair displays a maximum local degree of similarity, an& if the lengths of the given ...

In considering the degree of similarity that we expect by chance, these scoring functions allow us to compare two alignments by comparing their scores, but are less useful for assessing a pairwise alignment in an absolute sense. Given a pair of aligned sequences with a particular collection of matches, mismatches, and indels, does the alignment reflect enough similarity to suggest that it is of...

Biological sequence similarity analysis presents visualization challenges, primarily because of the massive amounts of discrete, multi-dimensional data. Genomic data generated by molecular biologists is analyzed by algorithms that search for similarity to known sequences in large genomic databases. The output from these algorithms can be several thousand pages of text, and is difficult to analy...

In the post-genomic era there has been an explosion in the amount of genomic data available and the primary research problems have moved from being able to produce interesting biological data to being able to efficiently process and store this information. In this paper we present efficient data structures and algorithms for the High Similarity Sequencing Problem. In the High Similarity Sequenc...

In biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an ”in vitro” sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the paramet...

In considering the degree of similarity that we expect by chance, these scoring functions allow us to compare two alignments by comparing their scores, but are less useful for assessing a pairwise alignment in an absolute sense. Given a pair of aligned sequences with a particular collection of matches, mismatches, and indels, does the alignment reflect enough similarity to suggest that it is of...

SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large datasets available it is now quite comm...

This paper presents a novel 2D shape classification approach, which exploits in this context the huge amount of work carried out by bioinformaticians in the biological sequence analysis research field. In particular, in the approach presented here, we propose to encode shapes as biological sequences, employing the widely known sequence alignment tool called BLAST (Basic Local Alignment Search T...