Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)

Basic local alignment search tool.

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. Th...

BLAST - an essential guide to the basic local alignment search tool

BLAT--the BLAST-like alignment tool.

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. Th...

Fast Semi-Local Alignment for DN 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...

PhAST: Pharmacophore alignment search tool

We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of mole...