MOTIVATION: Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures. RESULTS: We compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs. AVAILABILITY AND IMPLEMENTATION: All data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Scientific discovery relies on an experimental framework that corroborates hypotheses with experiments that are complex reproducible processes generating and transforming large datasets. The methods, implicit in the process, capture the semantics of the data, thus they are responsible for the generation of scientific information and discovery of scientific knowledge. Scientific workflows provide the semantics needed to wrap scientific data from their capture, analysis, publication, and archival. By annotating data with the processes that produce them, the scientist no longer manages data but information and allows their meaningful interpretation and integration. Any change to a scientific workflow may impact significantly the quality of the data produced, their semantics, their future analysis, use, integration, and distribution, as well as the performance of the execution. Yet, scientific workflows are typically transformed over time, updated with new versions of the tools that compose them, extended to new functionality, and composed. In this paper we discuss the various impacts of workflow transformation and illustrate them with a case study on the Structural Prediction for pRotein fOlding UTility System (SPROUTS) Workflow.

Since the early 1980s, protein/DNA sequence similarity search has become of major importance to biologists, and the need for fast and efficient tools grows with the size of databanks. Two programs use the strategy of finite state deterministic automatons to accomplish these searches. One of these two is BLAST, which is now widely used, and the other Automat, which has just been published. The differences and similarities in their basic principles, their use and their performances are analysed in this paper in order to allow optimal use of these important softwares.

Although various programs are available to extract all the information included in protein sequence databases, none is dedicated to immunoglobulins. For this purpose, we designed a program, SUBIM, which is adapted to the Kabat database specialized in immunoglobulin sequences. Besides all the possibilities of any database searching program, SUBIM analyses new sequences of variable regions and determines the variability subgroup they belong to. It also numbers the new sequence according to the system established by Kabat and co-workers for an easier comparison with the other immunoglobulins, thus realizing an automatic alignment with other members of a given type of immunoglobulin chain. This program is largely machine independent and requires very little memory, and should help biochemists concerned with new immunoglobulin sequences.