Applied Bioinformatics Course

Dotplot

• Dotlet - The Java based web server for the comparison of DNA and protein sequences using the dot plot approach, maintained by Swiss Institute of Bioinformatics.

Pairwise sequence alignment

• Align - The web server for the pairwise sequence alignment, maintained by EBI. Either global (Needle) or local (Water) alignment can be performed.
• BLAST 2 - The web server for the alignment of two sequences using BLAST maintained at NCBI.

Multiple sequence alignment

• ClustalW - The web server for the global multiple sequence alignment program maintained at EBI. It uses a new version of ClustalW 2.0.
• Muscle - The web server for the multiple sequence comparison by log-expectation, maintained at EBI. It claimed to achieve better accuracy with higher speed than ClustalW depending on the chosen options.
• MAFAT - The web server of high speed multiple sequence alignment using fast fourier transformation, maintained at EBI.
• KALIGN - The web server of fast and accurate multiple sequence alignment, maintained at EBI.
• TCoffe - The web server of several tools for computing, evaluating and manipulating multiple alignments of DNA and protein sequences and structures, developed and maintained by Cedric Notredame at Center for Genomic Regulation, Spain.
• Dialign - The web server for the multiple sequence alignment, developed and maintained by Burkhard Morgenstern at Bielefeld University, Germany. It uses a local alignment approach to compare whole segment of sequences without gap penalty.

Motif finding

• SMART - The web server for motif discovery and search, developed and maintained by University of California at San Diego. It provides
• MEME - The web server for motif discovery and search, developed and maintained by University of California at San Diego. It provides
• TMHMM - The web server for the prediction of transmembrane helices in proteins, developed and maintained by Denmark Technical University.

Gene identification

• GenScan - The web server for the identification of complete gene structures in genomic DNA, maintained by MIT.
• GenID - The web server o predict genes in anonymous genomic sequences , developed and maintained by University of Pompeu Fabra, Spain.
• HMMGene - The web server for the prediction of vertebrate and C elegans genes, developed and maintained by the Denmark Technical University.
• SoftBerry - The web server for gene prediction , limited free use for academic users.

Seuqence logo

• Weblogo - The web server for the generation of sequence logos, developed and maintained by University of California at Berkeley.

RNA secondary structure prediction

• MFOLD - The web server for the prediction of RNA secondary structure, developed and maintained by Michael Zuker at Rensselaer Polytechnic Institute.