[BiO BB] opinion of specialists

olga zelensky ozelensky at yahoo.ca
Thu Jan 17 11:29:08 EST 2002

Bioinformatics - a new direction in biology for me.
I'l be very appreciate to everybody for it's centences
about this plan.
With the best wishes

Plan of bioinformatics analysis of 
genes responsible for basement membrane formation

1.	Provide a Data Bases retrieval to determine
promoter structure of genes responsible for laminin
and collagen IV formation (human, mouse and puffer
2.	 Analysis of individual nucleotide sequences of
analyzed objects.
3.	 Multiple alignments of sequences at different
biological objects to determine homology between them.
4.	Statistical analysis of bases in analyzed
regulatory regions (frequency analysis and
distribution of every base, dinucleotide frequencies
and distribution, correlations within nucleotides for
the selected region of the sequence) to determine
their similarities and difference, and possible
connection between them. The correlation analysis for
analysis of aligned data sets for different groups of
genes in attempts to understand long-range
correlations in DNA sequences potentially associated
with specific in vivo structures during development
and differentiation.
5.	Investigation of regulatory regions of analyzed
genes. Analysis of specific sequence motifs in a set
of different genes to examine particular genomic loci
in depth, focusing on regions sharing synteny with
human chromosomes
6.	Genes mapping to analyze their spatial location and
it’s influence on regulatory function. 
7.	Comparative analysis of regulatory regions of
different genes to determine logic of their activity.
Analysis of specificity in bases sequences
(repetitions, periodicity etc.)
8.	Statistics of codons responsible for laminin and
collagen formation (base compositional bias between
codon positions,  periodicity in base occurrence) for
testing of hypothesis about genes concerted regulation
and for explanation their regulatory activity.
Frequency of usage of each codon (per thousand) in
human coding regions and the relative frequency of
each codon among synonymous codons. By comparing the
frequency of codons in a region of an species genome
read in a given frame with the typical frequency of
codons in the species genes, it is possible to
estimate a likelihood of the region coding. 
9.	Analysis of genes mutations in thickened basement
10.	Sequence analysis of  regulatory regions of genes
from health cells and those with thickened basement

Involved Data Bases :	BLAST, Compugen, EMBL, Ensemble,
Fasta, Gbase, GDB, GenBank, HUGEN, SWISS-PROT, The
Fugu Genomics Project, Mouse Gene,
Statistical Packages:  StatGraph, Costat,  Statistica, Jump

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