Here is a random collection of tools for biologists, written for the Web.

calc-amplicon -- show the region of a sequence that is amplified by two primers. Allow for mismatches.

calc-codons -- show all codons corresponding to a given peptide sequence. Very useful for designing degenerate primers...

calc-molar -- calculate number of picomoles given ng.

calc-ng -- calculate weight in ng from picomolar quantity.

chop-sequence -- Select a subregion of a sequence.

diff-JASPAR -- search for transcription factors in the JASPAR collection that bind better to one sequence than to another.

diff-TFD -- search for transcription factors in the TFD collection that bind better to one sequence than to another.

display-ds -- Display a sequence together with its complement.

motif-search -- Search for sequence motifs in DNA.

oligo-overlap -- Display the overlap between two oligos that are designed to anneal (for e.g. gel shift probes).

rc-sequence -- Make the reverse complement of the sequence (Note that chop-sequence will do this automatically for you if you put the larger coordinate first.)

reverse-sequence -- take a sequence and reverse its order, e.g. "GACC" goes to "CCAG".


Contact titus@caltech.edu if this stuff doesn't work or you have any suggestions.

You can also check out my Web page on bio-tools. Updates to this page will be posted to the mailing list on that page.