The copyrights of the programs in this page, such as BLAST, ClustalW/Probcons/Muscle, Exonerate and HMMER, belong to their authors. I am just adding the web interface to make them easy to run for myself and the public.

• A www interface for parsing BLAST output using the LIS (Longest Increasing Subsequence) algorithm

Process the BLAST result to find the longest consecutive list of HSPs. See my paper in Bioinformatics


• Multiple Sequence alignment

ClustalW is a classical and popular multiple sequence alignment program, while ProbCons is a great program according to the latest benchmark. MUSCLE is another good and fast alignment algorithm. Jalview can display alignments in a graphic interface and have lots of other functions, like phylogenetic tree

• Protein vs DNA alignment

A sequence alignment tool between a protein sequence and a DNA sequence using exonerate.

• Reverse Complement

Generate the reverse complement of a DNA sequence.

• DNA => peptide translation

Generate the peptide translation of a DNA sequence in multiple frames.

• Hidden Markov Model (HMM) Search using HMMER
  
  
  • Create HMM

  Create an HMM from a group of seed sequences

  • Search HMM

  Search an HMM against a list of sequences

• Many-to-many sequence comparison using BLAST

A tool to BLAST a group of query protein/DNA sequence against a group of target sequences. The results will be shown in an easily readable tabular form.

• Amino Acid Ratio

Calculate the percentage of amino acids content given a peptide sequence.