Home ~ Intro ~ Project ~ Script ~ Results ~ Conclusions ~ Links SNPs distribution in genes
Last Update: 21 March 2002
  1. Objectives
  2. Materials
  3. Methods


OBJECTIVES

We have studied the distribution of SNPs among human genome, locating them in exons, introns or splicing sites and distinguishing the lasts between donor and acceptor ones.

The project is focused basically on the relationship between SNPs and splicing sites due to the possibility that a SNP placed there may cause a differential splicing and, so on, a non functional protein. This would be the origin of disease or susceptibility to some factors in some instances.

SNPs location

Our objectives were:

  1. For every gene of the sequences folder, count the number of SNPs (total, in codificant regions and no codificant regions).
  2. Count the number of SNPs in splicing sites.
  3. Study the distribution of SNPs in human genome.



MATERIALS

The programs and the statistical analysis have been done in Perl language under Linux, a Unix-type operating system, while the web site has been done in HTML programming.

To work on the project we dispose of two data files:

All data was provided by R.Guigó, who processed it from Human Genome Project Working Draft ( Golden Path). The original file with the genes is refGene.txt.

Sequences data

The original information on refGene.txt is structured this way:

NM_gene|Chromosome|Strand|Start|End(transcript)|Start|End(CDS)|Number exons|Start&End exons

              Exemple:chr10 refseq cds 141296 141451 . + . NM_006624

And the folder we have worked with was designed in a more practical way, detailing the exons (CDS) for every gene (NM_gene) and chromosome.

Chromosome|refseq|CDS|Start CDS|End CDS|.|Strand|.|NM_gene

              Exemple: chr10 refseq cds 141296 141451 . + . NM_006624

SNPs data

We have two origin files, with the same structure:

Reference|Chromosome|Start SNP|End SNP|SNP_Reference

             Exemple:585 chr1 33352 33353 9493

The aspect that differences one from another is the way the data has been obtained: at snpNih.txt we find overlap SNPs, therefore they were placed studying the differences in nucleotide sequence between overlap contig clones, while at snpTsc.txt the SNPs were positioned with random genomic reads.


METHODS

The objective was comparing an SNP file with the refseq.gff one to obtain the location of SNPs in genes, sorting them into exons, introns, acceptors or donor sites and to make with them statistical analysis later. We have worked with snpNih.txt although the program is applicable to both files.

Actually we have obtained two programs, one of them made thanks to J.A Abril. The script done with his collaboration has a higher level and in our opinion is more interesting to explain how it works. If you want to see the script's explanation click here.

However, this program consumes more computer memory and has been impossible to run it at our usually available computers. As both programs return comparable results the final statistics analysis has been done with the results from our script.

Statistical analysis requires running the statistical module.





















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