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

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 …

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have
made important contributions to the theory of sequence database homology search …

Many theoretical advances have been made in applying probabilistic inference methods to
improve the power of sequence homology searches, yet the BLAST suite of programs is still …

The capacity of highly parallel sequencing technologies to detect small RNAs at
unprecedented depth suggests their value in systematically identifying microRNAs …

Sequence database searches require accurate estimation of the statistical significance of
scores. Optimal local sequence alignment scores follow Gumbel distributions, but …

Sequence similarity is a powerful tool for discovering biological function. Just as the ancient
Greeks used comparative anatomy to understand the human body and linguists used the …

The CATH database of protein domain structures (http://www. biochem. ucl. ac.
uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 …

We present a novel method for the comparison of multiple protein alignments with
assessment of statistical significance (COMPASS). The method derives numerical profiles …

Background For many RNA molecules, secondary structure rather than primary sequence is
the evolutionarily conserved feature. No programs have yet been published that allow …