• Publications
  • Influence
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detectionExpand
Pfam: the protein families database
Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries inExpand
What is dynamic programming?
  • S. Eddy
  • Medicine, Computer Science
  • Nature Biotechnology
  • 1 July 2004
TLDR
Sequence alignment methods often use something called a 'dynamic programming' algorithm, which can be a good idea or a bad idea, depending on the method used. Expand
The Pfam protein families database
TLDR
The latest version (4.3) of Pfam contains 1815 families, which match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. Expand
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
TLDR
This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Expand
Profile hidden Markov models
  • S. Eddy
  • Computer Science, Medicine
  • Bioinform.
  • 1998
TLDR
Profile HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise and complement standard pairwise comparison methods for large-scale sequence analysis. Expand
Initial sequencing and analysis of the human genome.
TLDR
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence. Expand
Accelerated Profile HMM Searches
  • S. Eddy
  • Computer Science, Medicine
  • PLoS Comput. Biol.
  • 1 October 2011
TLDR
An acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm, which computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. Expand
The Pfam protein families database: towards a more sustainable future
TLDR
Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set, and the facility to view the relationship between families within a clan has been improved by the introduction of a new tool. Expand
HMMER web server: interactive sequence similarity searching
TLDR
This work has focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. Expand
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