Jian Ye

TL;DR: Primer3’s current capabilities are described, including more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.

TL;DR: A new software tool called Primer-BLAST is presented to alleviate the difficulty in designing target-specific primers and combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers.

TL;DR: The sequence analysis tool IgBLAST is developed, which has the capability to analyse nucleotide and protein sequences and can process sequences in batches and allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.

TL;DR: Improvements to the BLAST report are described, design decisions are discussed, other improvements to the search page and database documentation are described and plans for future development are outlined.

TL;DR: The Basic Local Alignment Search Tool (BLAST) as discussed by the authors is a sequence similarity search program used by the National Center for Biotechnology Information (NCBI) to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence and integrate information about the database sequences from the NCBI Entrez system into the BLAST display.