BOAT: Basic Oligonucleotide Alignment Tool

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...

SOAP: short oligonucleotide alignment program

SUMMARY We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, sm...

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

AMOD: a morpholino oligonucleotide selection tool

AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design....

Vocabulary Alignment via Basic Level Concepts

Although significant overlap occurs in the semantic scope of existing thesauri and classification schemes, incompatibility between both the set of concepts they recognize and interrelationships among those concepts stands as a barrier to information exchange and integration, which, contrariwise, would be fostered by points of compatibility between systems. Preliminary research supported the pre...