ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. The online version is hosted by EMBL. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
lalign is a web app to compare two sequences looking for local sequence similarities. lalign/plalign use code developed by X. Huang and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the "sim" program. lalign will report a specified number of alignments (the default is 10) between the two sequences lalign shows the actual local alignments between the two sequences and their scores, while plalign produces a plot of the alignments that looks similar to a 'dot-matrix' homo
LALIGN/PLALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences. LALIGN shows the alignments and similarity scores, while PLALIGN presents a "dot-plot" like graph.
PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information and iteration capabilities.
The FFAS03 server provides an interface to the third generation of the profile-profile alignment and fold recognition algorithm FFAS. Profile-profile alignments utilize information present in sequences of homologous proteins to amplify the sequence conservation pattern defining the family resulting in detection of remote homologies beyond the reach of other sequence comparison methods. Input into the FFAS03 server is a protein sequence provided by the user. From the sequence a profile is generat
Consensus calculates the consensus for the CLUSTAL or MSF multiple alignment. Your alignment should be given in a file ( with complete path ) or directly in the following window. One can see and modify the default grouping of amino acids.
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.
PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities a