From: Gavin Sherlock <sherlock@genome.stanford.edu>
Date: September 30, 2005 2:38:21 GMT+02:00
To: Jacques van Helden <jacques.van.helden@ulb.ac.be>
Cc: Bruno André <bran@ulb.ac.be>, "'candida-curator@genome.stanford.edu' Curators" <candida-curator@genome.stanford.edu>
Subject: Re: WG: RSA-tools

Hi Jacques,

Here is an initial pass at the file you want - one version with all alleles, the other with just the haploid complement.  In the case of the file with all alleles, the two alleles that are from the same locus are consecutive in the file.  In each case the second allele for a locus comes from a contig whose name begins Contig19-20, so you can see the pairs of alleles in the file.  For the coordinates, the lowest coordinate is listed first, irrespective of the strand - if you'd like me to change it so that the first coordinate is 5' in the transcript, rather than the 5' in the contig, I can easily do that.  Finally, transcripts with exons only have the coordinates at their beginning and end, rather than the coordinates for each exon - I can change this, if you let me know the format that you would like it to be in,

Cheers,
Gavin

¨¨

On Sep 29, 2005, at 12:35 PM, Jacques van Helden wrote:

On Sep 29, 2005, at 20:32, Gavin Sherlock wrote:

Hi Jacques,

I am just starting to work on producing the tab delimited file that you need to load the C. albicans assembly 19, and have a few questions:

1.  For field 1, id, do you want our internal CGDID (available in our chromosomal features file, http://www.candidagenome.org/download/chromosomal_feature.tab), which for instance may look like CAL0001967, or do you want the orf19 identifier, which for instance may look like orf19.1137?

Both are suitable for me, as soon as they are unique (a single ID per feature).
If one of them is recognized as cross-reference by other databases as well, it is slightly better.
But in any case, I can also add the other ID as synonym in the file feature_names.tab.

2.  If for the id field you want the orf19 identifier, I presume that by feature name you mean the gene name (e.g. CDC8) if there is one?  Otherwise, I presume you mean the orf19 identifier.

Any alternative name is welcome. A single gene can be associated to various synonyms + to some universally  recognized IDs (e.g. transcript_id for mRNA, protein_id for CDS, GeneID for genes).

3.  C. albicans has a diploid assembly, which means that for many genes (though not all), there are two alleles.  Because they are represented by the same locus, the alleles will have the same CGDID, but have different orf19 identifiers.  For historical reasons, because of how the assembly was made, one of the alleles is generally considered to have precedence over the other, though in practice there should be no distinction between them.  Do you want the alleles represented in the tab delimited file, or would you prefer just of have the haploid set of genes?

This is a good question, and actually I have no idea about the answer.

I think I would need to do some trial to answer your question.
I would be tempted to ask you both versions. I would then start by comparing upstream sequences for the two alleles of each gene, in order to estimate the relevance of maintaining the two versions.

Actually, the fact to have two alleles might give us some clues about conservation of regulatory motifs, provided the differences are sufficient to show some divergence between non-regulatory non-coding sequences. I am not sure this will be the case, because the conservation is quie high even between different species of the same genus (e.g. Saccharomyces), but I would be tempted to measure it before taking a decision.

Thanks for your cooperativeness.

Jacques

Jacques van Helden <Jacques.van.Helden@ulb.ac.be>
http://www.scmbb.ulb.ac.be/~jvanheld/
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