Bioinformatics practicals
Click on the following links for Lab practicals for details
Database Search
Sequence similarity search against DNA or protein sequence database is one of the most extensively used approaches in the application of bioinformatics to molecular biology and genome research. Results of database search can deduce biological function for the newly identified sequence or to infer evolutionarily relationship among the query sequence and a group of matched subject sequences.
BLAST Search
• NCBI BLAST – the central point of the NCBI BLAST server which provides
whole functionality of DNA and protein sequence database search programs
including PSI-BLAST and PHI-BLAST and the whole list of databases in
different scales and different genomes.
• EBI BLAST – the entry page of the EBI BLAST facility which provides both
NCBI BLAST and WU-BLAST programs as well as a set of specialized BLAST programs to search the alternative splicing database, the cloning vector database, and the parasite database.
• Sanger BLAST – the entry page of the sequence projects BLAST search services at the Sanger Institute, featured with the special genome databases generated by the completed or ongoing sequencing projects.
Other Database Search
• FASTA – the original website for the FASTA set programs maintained by
William Pearson at the University of Virginia. It provides extensive documents
and help materials as well.
• EBI FASTA – the entry page of EBI FASTA services. FASTA has a higher
sensitivity in some cases comparing with BLAST with a slightly lower speed. It
is specific to identify low similarity long regions for highly diverged sequences.
• GoldenPath BLAT – the web server for the genome database search, integrated in the GoldenPath platform.
• ENSEMBL BLAT – the web server for the genome database search, integrated in the ENSEMBL platform
Sequence Analysis
DNA and protein sequence analysis are the most fundamental approach in bioinformatics.
Dotplot
• Dotlet – the Java-based web server for the comparison of DNA and protein
sequences using the dot plot approach, maintained by the 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.
• T-Coffee – 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 the 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 a whole segment of sequences without gap penalty.
Gene Identification
• GENSCAN – the web server for the identification of complete gene structures in genomic DNA, maintained by MIT
• GenID – the web server for the prediction of genes in anonymous genomic
sequences, developed and maintained by the 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