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=BIOL 302 Lab (Bioinformatics Exercises)=
*[[NOTE: Link to BIOL302 page, if one exists]]
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==
<div class="center" style="width:auto; margin-left:auto; margin-right:auto;">
[[File:4seq.png]]

''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.''
</div>
===[[QuBi/modules/biol302#Objectives|Objectives]]===
* Learn to use Genbank database and BLAST tool to analyze nucleotide sequences
* Use BLAST to identify 

===[[QuBi/modules/biol302#Key Concepts|Key Concepts]]===
====Blast====
====Alternative Splicing====


===[[QuBi/modules/biol302#Exercise|Exercise]]===

*[[NOTE: Maybe we should remove the "Description" section of this table and leave it up to the students to figure out which exons are missing]]
{| class="wikitable"
! 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, including its introns/exons, 3'/5' UTRs, +1. (Note: this diagram is going to be very handy for the last set of questions.)
- Label each feature with its coordinates. For example, if an exon starts at 500bp and ends at 1000bp, label it as such.
- Label the diagram with basic information, such as the gene's name and th organism's species.  
- The drawing does not have to be exactly to scale, a reasonable effort should be made to do so. Put length markers on your drawing (for example, every 5000bp.)
- The mRNA annotation states which segments are used to create mRNA, and the CDS annotation states which parts actully code amino acids (CDS = coding sequence).
# 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?


===[[QuBi/modules/biol302#Exit_Questions|Exit Questions]]===