HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling.

Motivation: The HHsearch algorithm, implementing a hidden Markov model (HMM)-HMM alignment method, has shown excellent alignment performance in the so-called twilight zone (target-template sequence identity with ∼20%). However, an optimal alignment by HHsearch may contain small to large errors, leading to poor structure prediction if these errors are located in important structural elements.

Results: HHalign-Kbest server runs a full pipeline, from the generation of suboptimal HMM-HMM alignments to the evaluation of the best structural models.

Detecting protein candidate fragments using a structural alphabet profile comparison approach.

Predicting accurate fragments from sequence has recently become a critical step for protein structure modeling, as protein fragment assembly techniques are presently among the most efficient approaches for de novo prediction. A key step in these approaches is, given the sequence of a protein to model, the identification of relevant fragments - candidate fragments - from a collection of the available 3D structures. These fragments can then be assembled to produce a model of the complete structure of the protein of interest.

GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'.

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies.

Results: Different services are provided like the possibility of inferring a phylogenetic tree with sequence signatures or comparing two genomes and displaying the rearrangements that happened since their separation.