Zhang, Hongyu


	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 Create HMM Create an HMM from a group of seed sequences Search HMM Search an HMM against a list of sequences All-against-all 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.