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Tools

  • BLAST - NCBI  •  The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.  [less]
  • BLAST - PBIL  •  BLAST search on protein sequence databases [less]
  • Blast2Fasta  •  Converts BLAST output from NCBI to FASTA format. [less]
  • FASTA/SSEARCH/GGSEARCH/GLSEARCH  •  This tool provides sequence similarity searching against protein databases using the FASTA suite of programs. FASTA provides a heuristic search with a protein query. FASTX and FASTY translate a DNA query. Optimal searches are available with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).  [less]
  • LALIGN  •  LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally. [less]
  • Phylogibbs  •  Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy. [less]
  • SAMBA  •  SAMBA is a 128 processor array for speeding up the comparison of biological sequences. The hardware implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty. [less]
  • Sequerome  •  Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. [less]
  • WU BLAST  •  Protein databases query to find regions of sequence similarity quickly, with minimum loss of sensitivity.  [less]