Attendance: Lenny Heath, John Hanks, Ranjit Randhawa, John Archie, Ceci Vasquez-Robinet, Rob Stclair, Naren Ramakrishnan, Ruth Grene
Discussed plans for the summer. Dr Grene handed out questions to focus research on
Main steps:
- Given gene family, e.g.. Superoxide Dismutase (SOD)
- Look upstream
- Find regulatory sequences (can occur in different permutations and combinations)
Four main points of the meeting were:
We will be given gene families to look at. The Superoxide Dismutases (SOD) genes was already studied about. There are 7 genes in total. Two have been found to contain both HRE and ARE in their upstream sequences. There is a paper that came from that at the expresso publications site. Dr. Grene and Ceci will be giving you more Arabidopsis gene families to investigate.
- Given a list of regulatory sequences provide a catalogue with respect to where they occur within the SOD gene family.
- We would also like to find the chromosome locations of all these elements for possible future work.
- Use the promoter database to verify results obtained.
Dr heath went into detail about the formats of GenBank and FASTA files and how one should parse them.
FASTA files have a header line of information and then the nucleotide sequence GenBank file have more information, keywords include LOCUS,ORGANISM,FEATURES, etc. Under features (if one refers to a chromosome) there will be a list of genes.
E.g.
FEATURE
gene 51..2011 //position in sequence
mRNA join(60..89, 600..790,..) //experimentally verified
CDS join(70..85, 110..500,..) //coding strand (prediction of intronless sequence)
When dealing with genes on complementary strands knowing where the upstream region occurs is important. One can find the following in a GenBank file gene complement(5000..7000)
E.g.
Two complimentary strands with genes
Note: Gene 2 is on the complimentary strand
gene2 5'------------------|--\ORF2\--|----|--|----------3' | | | gene1 | | | gene3 3'-----|--\ORF1\--|---------+-------|--\ORF3\--|--5' | | | | |<---------| |------>|->| upstream region of gene1 upstream region of gene2
Upstream region ALWAYS starts from the start of the ORF (that is, just before the START codon).
Upstream region can end either at the beginning of the next gene or the beginning of the next ORF.
People doing different things:
- John A will focus on post processing.
- Dr Ramakrishnan will focus on modeling and will look at the databases
- John H will work with Dr Ramakrishnan
- Rob and Ranjit met with Dr Grene (on Thursday). Dr Grene told us to look at chromosome 4 for specific elements and catalogue them.