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Help Home > Alignment Search > Running an Alignment Search > Specifying Search Criteria

BLAST query page panel header: squery sequences Search Criteria BLAST query page panel header: program settings BLAST query page panel header: organisms

The Alignment Query Page: Specifying Search Criteria

Alignment Programs

Alignment searches may be run using a variety of programs which compare DNA, protein, or translated nucleotide sequences. These programs are based on three families of alignment algorithms, NCBI's BLAST, Webb Miller's Blastz , and Jim Kent's BLAT (BLAST-Like Alignment Tool).

BLAST query Search Criteria panel

For more information about the difference between the two algorithms and their variations see:

Databases

BLAST query databases

With each of our organism sites we provide a number of target databases for alignment search which may include:

  • All Assemblies available for the organism
  • ESTs
  • All Models: protein and transcript files for predicted gene models in all model tracks
  • Default analysis track: protein and transcript files for predicted gene models in the default analysis track(e.g. GeneCatalog or FilteredModels)
  • Masked Assemblies: Repeat-masked assemblies for the organism