Exam 1 for Bioinformatics for Biologists

Match the NCBI resource with its description: 3 points each

1. DNA and RNA sequences from GenBank and RefSeq
2. Taxonomic classification and nomenclature catalog
3. Genome sequencing projects by organism
4. Collected information about gene loci
5. Functional genomics studies
6. Short genetic variations
7. Human variations of clinical significance
8. Protein sequences from GenBank and RefSeq
9. Scientific and medical abstracts/citations
10. Genotype/phenotype interaction studies

Acquire the complete mitochondrion genome for Mus musculus from NCBI (NCBI Reference Sequence: NC_005089.1). Identify protein-coding regions in that sequence using NCBI’s ORF-Finder. From this program’s output, please answer the following questions: (5 points each)

Analyze the mitochondrion genome for Mus musculus with tRNAscan-SE. From this program’s output, please answer the following questions:

Acquire the complete genomic sequence of Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, NCBI Reference Sequence: NC_002127.1, from NCBI. Use this sequence to perform the following: (5 points each)

1. Use fgenesB from Softberry for bacterial operon and gene prediction
2. Use BPROM from Softberry for prediction of bacterial promoters
3. Use FindTerm from Softberry for finding terminators in bacterial genomes