Applied Bioinformatics Course

Gene structure analysis and prediction

• Draw the gene structure of the Drosophila melanogaster homologue of human Down syndrome cell adhesion molecular (DSCAM) (AF260250).
• Predict the potential genes from the fugu cosmid sequence [af164138.fasta]
• Draw the exon/intron structure of the Arabidopsis SBP gene [At2g47070] with the gene struture dispaly system (GSDS) and compare the results with that of NCBI Gene database and TAIR annotation.

Sequence composition

• Find GC content of 2 pairs of rice sequence fragment, draw a plot [rice-pair1.fasta, rice-pair2.fasta].
• Find the CpG island of the fugu cosmid sequence [af164138.fasta].
• Calculate the Codon usage of the coding sequence of fugu MDR3 [fugu-mdr3-cds.fasta].
• Calculate the GC content of coding and non-coding sequences of fugu cosmid [af164138-cds.fasta, af164138-ncs.fasta].

Secondary structure

• Predict the tandem repeat of the human herpesvirus 7 gene locus (HH7TETRA).
• Predict the secondary structure of human mitochondria tRNA-Leu (AB026838).