Alu and You - in silico
Integration of PV92 Human Alu Insertion Polymorphism DNA lab with PV92 Bioinformatics
(Keywords: PV92; Alu; electronic PCR; ePCR; in silico PCR)
- Identify and gather targets ('hits') through ePCR
- Perform Blast search with forward primer
- Collect search 'hits'
- Delimit sequences by aligning them with reverse primer
Alternatively: work with sequences in Sequence Server ('Manage Groups', change 'Classes' -> 'Public', check box for 'PV92 ePCR', select 'OK')
- Determine relationships among 'hits'
- Identify shared regions and dissimilar regions.
- Determine nature of differences.
- Put together findings to determine relationships among all 'hits'.
Alternatively: determine relationships among the three sequences through this view of the relationships of any two 'hits'
- Determine Alu insertion status of students' PV92
- DNA isolation
- DNA amplification
- Gel electrophoresis
- Determine status of each student in class
- Enter results into Allele Server
Alternatively: there is no alternative to performing the wet lab in order to determine your students' genotypes
- Determine allele status of class and compare with that of other populations
- Analyze occurrence of derivate allele and genotypes in class
- Examine results using Chi2 and Hardy-Weinberg analysis
- Compare results of class with those found for other world populations
Alternatively: compare the genotypes in the list of references in Allele Server and examine the distribution of genotype frequencies across the world
- Locate PV92 locus in human genome
- Perform Blast search on entire human genome utilizing a non-Alu sequence stretch from one of the previous 'hits'
- Identify locus within human genome
- Examine which genes are surrounding locus
- Examine whether locus falls into a gene
- Examine sequence of locus in human genome to verify identity with query
Alternatively: there is no real alternative to this
- Identify other Alu elements
- In Genbank
- Perform Blast Search with the three insertions identified in PV92 (315 nt; 346 nt; 659 nt)
- Analyze 'hits'
- Develop Alu phylogenetic tree
Alternatively: check this web page for some results of a respective Blast search on genbank.
- In the human genome
- Perform Genbank search (Nucleotide) with these search term combinations:
- NF1 AND homo AND sapiens AND Alu
- Huntingtin AND homo AND sapiens AND Alu
- ADA AND homo AND sapiens AND Alu
- Examine the Genbank entries for your search 'hits' and compare and contrast your findings with the LocusLink and OMIM entries for NF1, Huntington and ADA Deficiency. What chromosomes are the genes involved in these deficiencies located on. How long are the genes and how are they structured?
Alternatively: there is no real alternative to this
