A Global Iterations Method for Recreating Railway Vertical Alignment Considering Multiple Constraints

Global Multiple Sequence Alignment

As with pairwise alignment, multiple sequence alignments (MSAs) are typically scored by assigning a score to each column and summing over the columns. The most common approach to scoring individual columns in a multiple alignment is to calculate a score for each pair of symbols in the column, and then sum over the pair scores. This is called sum-of-pairs or SP-scoring. For global multiple seque...

A Global Method for Crew Planning in Railway Appli ations

MuSiC: a tool for multiple sequence alignment with constraints

SUMMARY MuSiC is a web server to perform the constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned with each other. The input of the MuSiC system consists of a set of protein/DNA/RNA sequences and a set of user-specified constraints, each with a fragment of residue/nucleotide that (approximately) appears in all input sequences. The output of ...

A memory-efficient algorithm for multiple sequence alignment with constraints

MOTIVATION Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficientl...

gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences

Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...