Number of sequences in database

[James]

I've been using SLiMSearch3 for looking at motif conservation and have found it very helpful. One question I have: how many sequences are in the human database that is being queried? For instance, for one of my motifs it reports 2562 instances in 2101 proteins, but I'd like to know out of how many total proteins this refers to, to find out if the motif I have is enriched in my dataset, relative to the whole proteome.

I can't seem to find this information. In the SLiMSearch2 paper in mentions the Uniprot release v1.37, but I'm not sure where to get this or if there is a new release that is being searched.

Thanks for the help.

James

[Niall Haslam]

Hi James,

Thanks for your comments.

The uniprot release used has 20284 proteins, however, due to some filtering for sequences that it is impossible to align there are effectively only 20258 proteins in the final search database. If you want I can send you on a list of the UniProt Ids?

Niall

James

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[James]

Thanks Niall, that's perfect, I just needed to know the total number of proteins.

James

On Thursday, November 22, 2012 2:47:43 PM UTC-5, Niall wrote:

Hi James,

Thanks for your comments.

The uniprot release used has 20284 proteins, however, due to some filtering for sequences that it is impossible to align there are effectively only 20258 proteins in the final search database. If you want I can send you on a list of the UniProt Ids?

Niall

On 22 November 2012 18:33, James <knig...@gmail.com> wrote:

I've been using SLiMSearch3 for looking at motif conservation and have found it very helpful. One question I have: how many sequences are in the human database that is being queried? For instance, for one of my motifs it reports 2562 instances in 2101 proteins, but I'd like to know out of how many total proteins this refers to, to find out if the motif I have is enriched in my dataset, relative to the whole proteome.

I can't seem to find this information. In the SLiMSearch2 paper in mentions the Uniprot release v1.37, but I'm not sure where to get this or if there is a new release that is being searched.

Thanks for the help.

James

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