ALSCRIPT: a tool to format multiple sequence alignments

ALSCRIPT: a tool to format multiple sequence alignments.

PROMALS3D: a tool for multiple protein sequence and structure alignments

Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural informat...

Multiple Sequence Alignments in Linguistics

In this study we apply and evaluate an iterative pairwise alignment program for producing multiple sequence alignments, ALPHAMALIG (Alonso et al., 2004), using as material the phonetic transcriptions of words used in Bulgarian dialectological research. To evaluate the quality of the multiple alignment, we propose two new methods based on comparing each column in the obtained alignments with the...

Evolving Better Multiple Sequence Alignments

Aligning multiple DNA or protein sequences is a fundamental step in the analyses of phylogeny, homology and molecular structure. Heuristic algorithms are applied because optimal multiple sequence alignment is prohibitively expensive. Heuristic alignment algorithms represent a practical trade-off between speed and accuracy, but they can be improved. We present EVALYN (EVolved ALYNments), a novel...

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-...