Stephen F. Altschul

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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 s...

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

We describe an approach to analyzing protein sequence databases that, starting from a single uncharacterized sequence or group of related sequences, generates blocks of conserve...

Basic local alignment search tool

Basic Local Alignment Search Tool

Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to deciphering these sequences and understanding ...

Amino acid substitution matrices from an information theoretic perspective

[27] Local alignment statistics

Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST

TBLASTN is widely used, as it is common to wish to compare proteins to chromosomes or to libraries of mRNAs. Composition-based statistics improve the statistical accuracy, and t...