Pattern discovery in yeast downstream sequences

Pattern discovery in yeast downstream sequences
Supplementary material for the article :
van Helden, J., Olmo, M. & Perez-Ortin, J. E. (2000). Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 28(4), 1000-1010. Pubmed 10648794

Data

Sequences

Downstream sequences Positions relative to stop codon: position +1 is the first nucleotide after the coding sequence, negative coordinates indicate coding sequences.

Intergenic segments All yeast intergenic sequences, separated in 3 subsets:

tandem : interrgenic sequences between two genes transcribed in the same direction
divergent: intergenic sequences between the start codon of two genes transcribed in opposite and divergent direction
convergent: intergenic sequences between the stop codons of two genes transcribed in opposite and converent direction

Sequences around cleavage sites Sequences kindly provided by Joel Graber. Sequences around cleavage sites, located by mapping EST segments onto the genomic sequences. See Graber's paper for details.
Graber JH, Cantor CR, Mohr SC, Smith TF. Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Res. 1999 Feb 1;27(3):888-94. Pubmed 9889288

Subsets Selections of sequences according to various criteria (see paper for details)

Results

Discovered oligonucleotides

Analysis of all downstream sequences

Over-represented oligos Statistical estimation of oligo over-representation, using a Markov chain background model.

Positionally biased oligos Detection of oligonucleotides having a positional bias, e.g. a distribution with peaks of valleys.

Analysis of all sequences around cleavage sites

Over-represented oligos Statistical estimation of oligo over-representation, using a Markov chain background model.

Positionally biased oligos Detection of oligonucleotides having a positional bias, e.g. a distribution with peaks of valleys.

The main files are indicated above. The other files are not indexed, but their name generally indicates their content.
In case of trouble, please contact Jacques van Helden

Downstream sequences	Positions relative to stop codon: position +1 is the first nucleotide after the coding sequence, negative coordinates indicate coding sequences.
Intergenic segments	All yeast intergenic sequences, separated in 3 subsets: tandem : interrgenic sequences between two genes transcribed in the same direction divergent: intergenic sequences between the start codon of two genes transcribed in opposite and divergent direction convergent: intergenic sequences between the stop codons of two genes transcribed in opposite and converent direction
Sequences around cleavage sites	Sequences kindly provided by Joel Graber. Sequences around cleavage sites, located by mapping EST segments onto the genomic sequences. See Graber's paper for details. Graber JH, Cantor CR, Mohr SC, Smith TF. Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Res. 1999 Feb 1;27(3):888-94. Pubmed 9889288
Subsets	Selections of sequences according to various criteria (see paper for details)

Analysis of all downstream sequences
Over-represented oligos	Statistical estimation of oligo over-representation, using a Markov chain background model.
Positionally biased oligos	Detection of oligonucleotides having a positional bias, e.g. a distribution with peaks of valleys.
Analysis of all sequences around cleavage sites
Over-represented oligos	Statistical estimation of oligo over-representation, using a Markov chain background model.
Positionally biased oligos	Detection of oligonucleotides having a positional bias, e.g. a distribution with peaks of valleys.