Possibly useful programs for filtering sequences

Gene finders
Similarity finders
DNA feature finders
Protein feature finders
Pattern finders
Miscellaneous tools
Commercial sites

Gene Finders

Similarity Finders      How to confine searches to specific databases or specific organisms This is often a good idea in order to get more accurate E values or because you're interested only in hits within a specific class of sequences. Or you may want to search only cDNA, in order to figure out exon/intron structure. There are many ways to get the job done: DNA Feature Finders PROTEIN Feature Finders Pattern Finders Examples of user-specified patterns (click here for complete list of one-letter codes)
looks for AvaI sites (Y=pyrimidine, R=purine)
looks for AvaII sites (W=A or T)
looks for consensus prokaryotic promoter (two 6-base sequences separated by 16 to 18 bases)

Miscellaneous Tools

  • Molecular Toolkit [http://arbl.cvmbs.colostate.edu/molkit/index.html] (Colorado State University)
    Many tools for quick manipulation of DNA and protein sequences: Inverse, translate, reverse translate, hydrophobicity plots, dot plots.
  • Addendum: Commercial Sites

    Many companies sprung out with the genomic fever, offering integrated gene finding services. Below is a list of some of these companies (in alphabetical order). They are still evolving, some might continue this line of business the market permitting, others might turn into pharmaceutical companies on their own and others might simply disappear. The list is just for your information and in no way implies an endorsement from our part on any of them.

    Celera Discovery System (CDS) [http://www.celera.com/index.cfmhttp://www.celera.com/index.cfm], Celera Genomics.

    LifeSeq®[http://www.incyte.com/#], Incyte Genomics.

    genomeSCOUT®[http://www.lionbioscience.com/solutions/genomescout], LION Bioscience.

    Rosetta Resolver® System [http://www.rosettabio.com/home.html], Rosetta Inpharmatics (acquired by Merck).