YASS: enhancing the sensitivity of DNA similarity search - PubMed (original) (raw)

Laurent Noé et al. Nucleic Acids Res. 2005.

Erratum in

Abstract

YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant alignments. A web interface (http://www.loria.fr/projects/YASS/) is available to upload input sequences in fasta format, query the program and visualize the results obtained in several forms (dot-plot, tabular output and others). A standalone version is available for download from the web page.

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Figures

Figure 1

Figure 1

The input window (A) allows users to control most YASS parameters, from most basic to more advanced. Results are output in tabular format (B), with the possibility of displaying each sequence alignment (C).

Figure 2

Figure 2

Three YASS dot-plots are shown, each obtained from pairs of closely related bacterial sequences. Green segments represent alignments of forward reads and red segments correspond to alignments between the reverse complement of one sequence and the forward read of the other.

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