Group DNA: Groups DNA into blocks of chosen length and numbers lines.
Show Translation: By far my favorite amino acid/nucleotide output. Copy/pastes well into Word docs.
Filter Protein/Group Protein: Remove non-amino acid characters/group with spaces and number, as above for DNA.
BLAST
blastn: align 2 or more nucleotide sequences
note: I recommend viewing multiple alignments by reformatting the results page using the menu at the top of the page:
tblastn: align a protein sequences with one or more nucleotide sequences
Useful for checking sequencing results if you only care about amino acid changes, will align in all 6 reading frames so you can check forward and reverse primers at the same time.
blastx: search protein databases with nucleotide sequence
Useful for determining what you've pulled up with sequencing results when it doesn't match an expected sequence. If you get a lot of nonsense results, you've probably pulled part of a common vector component.
Cloning
NEBcutter V2.0 is a great web-based restriction digest tool. It will find all restriction sites in a given sequence, calculate lengths based on linear or circular DNA, and can also provide a list of 0- or 1-cutter enzymes.
