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Sequences on [[genbank]] have both basic reference information (such as what the sequence is, what organism it came from, and bibliographical information) and sequence [[annotations]]. Some sequences are more richly annotated than others - it is up to researchers to annotate the sequences they generate, which requires extra work. For this exercise you will be working will a well-annotated sequence: [[accession number]] AF527840. Explore its annotation and use it to complete the following set of tasks. | Sequences on [[genbank]] have both basic reference information (such as what the sequence is, what organism it came from, and bibliographical information) and sequence [[annotations]]. Some sequences are more richly annotated than others - it is up to researchers to annotate the sequences they generate, which requires extra work. For this exercise you will be working will a well-annotated sequence: [[accession number]] AF527840. Explore its annotation and use it to complete the following set of tasks. | ||
# DRAW a diagram of this gene | # DRAW a diagram of this gene using the information and coordinates listed in the annotation. (Note: this is the bulk of the assignment and this diagram is needed for the last set of questions. Don't get lazy on this.) | ||
##Label the top of the diagram with basic information, such as the gene's name, organism, etc.. Someone should be able to pick up your diagram and know exactly what they're looking at. | |||
##Including introns, exons, 3'/5' UTRs, +1, and exact coordinates. The mRNA annotation states which segments are used to create mRNA, and the CDS annotation states which parts code amino acids (CDS = coding sequence). | |||
##Draw the diagram mostly to scale. It does NOT have to be perfect, but make a reasonable effort. Put a scale bar and length markers on your drawing. | |||
# How does the sequence vary at positions X, X, and X for this gene? | # How does the sequence vary at positions X, X, and X for this gene? | ||
# What kinds of repeat regions can be found in this gene? | # What kinds of repeat regions can be found in this gene? | ||
Revision as of 17:38, 21 February 2013
- BIOL 302 Lab (Bioinformatics Exercises)
Research in molecular genetics requires effective use of bioinformatic tools to analyze and understand the genetic materials being worked with. The following exercises will expose you to real-world scenarios and introduce you to the methods and tools you can use to solve these problems.
Identification of mdm2 Splice Variants Using BLAST
A diagram of the gene used in this exercise and its splice variants. By the end of this module you will create a similar diagram.
Objectives
- Learn to use Genbank database and BLAST tool to analyze nucleotide sequences
- Use BLAST to identify
Key Concepts
- Blast
- Genbank
- Annotation
- Accession Number
- Alternative Splicing
Exercise
| Genbank Accession # | cDNA Clone | Description | Cell Line | Length (bp) |
|---|---|---|---|---|
| AF527840 | Genomic DNA | 34,088 | ||
| EU076746 | P2-MDM2-C1 | cDNA missing exons 5-9 & 11 | MANCA | 427 |
| EU076747 | P2-MDM2-10 | cDNA missing exon 10 | ML-1 | 842 |
| EU076748 | P2-MDM2-C | cDNA missing exons 5-9 | A876 | 505 |
| EU076749 | P2-MDM2-FL | Full-length cDNA | SJSA-1 | 845 |
- Explore the gene annotation for AF527840.
Sequences on genbank have both basic reference information (such as what the sequence is, what organism it came from, and bibliographical information) and sequence annotations. Some sequences are more richly annotated than others - it is up to researchers to annotate the sequences they generate, which requires extra work. For this exercise you will be working will a well-annotated sequence: accession number AF527840. Explore its annotation and use it to complete the following set of tasks.
- DRAW a diagram of this gene using the information and coordinates listed in the annotation. (Note: this is the bulk of the assignment and this diagram is needed for the last set of questions. Don't get lazy on this.)
- Label the top of the diagram with basic information, such as the gene's name, organism, etc.. Someone should be able to pick up your diagram and know exactly what they're looking at.
- Including introns, exons, 3'/5' UTRs, +1, and exact coordinates. The mRNA annotation states which segments are used to create mRNA, and the CDS annotation states which parts code amino acids (CDS = coding sequence).
- Draw the diagram mostly to scale. It does NOT have to be perfect, but make a reasonable effort. Put a scale bar and length markers on your drawing.
- How does the sequence vary at positions X, X, and X for this gene?
- What kinds of repeat regions can be found in this gene?