The BLAST programs are widely used tools for searching protein and DNA databases for
sequence similarities. For protein comparisons, a variety of definitional, algorithmic and�…

PSI-BLAST is an iterative program to search a database for proteins with distant similarity to
a query sequence. We investigated over a dozen modifications to the methods used in PSI�…

Almost all protein database search methods use amino acid substitution matrices for
scoring, optimizing, and assessing the statistical significance of sequence alignments. Much�…

Background The molecular cause of inflammatory bowel disease is largely unknown.
Methods We performed genetic-linkage analysis and candidate-gene sequencing on�…

Linkage analysis using maximum-likelihood estimation is a powerful tool for locating genes.
As available data sets have grown, the computation required for analysis has grown�…

Motivation: The BLAST software package for sequence comparison speeds up homology
search by preprocessing a query sequence into a lookup table. Numerous research studies�…

Background The hyper-IgE syndrome (or Job's syndrome) is a rare disorder of immunity and
connective tissue characterized by dermatitis, boils, cyst-forming pneumonias, elevated�…

Background Chronic mucocutaneous candidiasis may be manifested as a primary
immunodeficiency characterized by persistent or recurrent infections of the mucosa or the�…

The protein cytotoxic T lymphocyte antigen-4 (CTLA-4) is an essential negative regulator of
immune responses, and its loss causes fatal autoimmunity in mice. We studied a large family�…

Many algorithms for NP-hard optimization problems find solutions that are locally optimal, in
the sense that the solutions cannot be improved by a polynomially computable perturbation�…