MULTAN: a program to align multiple DNA 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...

Using a Tabu Search Approach to Align DNA Sequences

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...

MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance ...