Homology/Pattern Search
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Detection and alignment of repeats in protein sequences
RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Genome Engineering
Addgene is working with the leading scientists in the field to assemble the reagents and information you need to use the CRISPR/Cas9 technology in your own lab.
We describe a method for efficiently creating mutations in chosen Drosophila genes within a month based on the CRISPR/Cas9 system from bacteria.
Submit multiple sequences in Fasta format for CRISPR design and analysis.
or
Submit a single sequence for CRISPR design and analysis.
Structure Predictions
Protein Structure Visualization
PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing an incentive copy, which is pre-built and comes with maintenance and support.
Here you will learn all the latest and greatest techniques for making movies in PyMOL. These make you look like a master of PyMOL when you can show them off in a presentation or even in MPEG/AVI format. For your ease of learning I have commented all of the movie scripts and tried to ensure that they work in PyMOL if you just copy/paste the code.
Multiple Sequence Alignment
-multiple sequence and structure alignment server