BackgroundSequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.ResultsWe describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site.ConclusionThe new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.

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In recent years the increased use of 3D scanning hardware has introduced a new type of data to the design and manufacturing field. In many design and manufacturing applications (e.g., part refurbishing or remanufacturing) a scanned 3D model may be provided as an input to a shape matching system to search the database for related or identical models with the purpose of extracting useful information. The introduction of scanned 3D models restricts the use of the CAD-based 3D model search and comparison methods due to significant differences in model representations. The CAD models provide structured and high-level representation of the part features, whereas the scanned 3D models usually come in a polygonal mesh representation, which does not directly reveal engineering features of the part. These differences require new algorithms for comparing the shapes of scanned 3D models, ones that are robust against different scanning technologies and can be adjusted to work with different representations of the models. In this paper, a new approach and algorithms for scanned 3D shape matching and comparison are presented. Given the scanned 3D model as an input the approach first uses general-purpose shape matching methods to identify a small list of likely matches (i.e., candidate models) for more detailed shape comparison. To perform detailed comparison of the shapes each candidate model is geometrically adjusted (i.e., rotated and translated) with the input using one of two new viewpoint algorithms developed in this paper. Once the candidate models are adjusted they are compared to the input to identify the similarities and differences between their shapes. To accomplish this task a new 3D shape matching algorithm is developed. The relevance of the methodology developed in this paper is illustrated with the application of scanned 3D shape matching and comparison algorithms in rapid manufacturing of broken parts.

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