[BiO BB] opinion of specialists

shure shure at mail.ru
Fri Jan 18 15:14:55 EST 2002


извини за краткость, но английский плох... *на мой взгляд, конечно)
не говоря уже о
oz> I'l be very appreciate to everybody for it's centences
oz> about this plan.


Thursday, January 17, 2002, 5:29:08 PM, you wrote:

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

oz> Plan of bioinformatics analysis of 
oz> genes responsible for basement membrane formation

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

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

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Best regards,
 shure                            mailto:shure at mail.ru

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