PASS: a program to align short sequences

MULTAN: a program to align multiple DNA sequences

I describe a computer program which can align a large number of nucleic acid sequences with one another. The program uses an heuristic, iterative algorithm which has been tested extensively, and is found to produce useful alignments of a variety of sequence families. The algorithm is fast enough to be practical for the analysis of large number of sequences, and is implemented in a program which...

EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA

This note describes the program EST_GENOME for aligning spliced DNA to unspliced genomic DNA. It is written in ANSI C and has been tested under Digital OSF3.2. The spurce code and documentation are available from ftp:// www.sanger.ac.uky ftp/pub/ badger/est_genome.2.tar.Z. The prediction of genes in uncharacterized genomic DNA sequence is currently one of the main problems facing sequence annot...

BlastAlign: a program that uses blast to align problematic nucleotide sequences

UNLABELLED BlastAlign uses NCBI blastn to build a multiple nucleotide alignment and is intended for use with sequences that have large indels or are otherwise difficult to align globally. The program builds a matrix representing regions of homology along the sequences, from which it selects the 'most representative' sequence and then extracts the blastn query-anchored multiple alignment for thi...

Using a Tabu Search Approach to Align DNA Sequences

Learning to Align Sequences: A Maximum-Margin Approach

We propose a discriminative method for learning the parameters of linear sequence alignment models from training examples. Compared to conventional generative approaches, the discriminative method is straightforward to use when operations (e.g. substitutions, deletions, insertions) and sequence elements are described by vectors of attributes. This admits learning flexible and more complex align...