Mapping Of Uniprot Ids To Mips Ids

Question

[Sirus]

Hello every body, I have a list of proteins ID in Uniprot format and I want to have their IDs in the MIPS database, could any one point me how to do it? I am still a beginner in this field, Thank you in advance.

[Dave Bridges]

I was about to suggest BioMart, but strangely there is no MIPS attribute there. Thats what i would generally use for these sorts of things

[Pawel Szczesny]

Dave, isn't that connected to the fact that MIPS services are notoriously unreliable? At this moment ca. half of their databases/web apis are unavailable or broken.

[Neilfws]

I'm confused: I thought MIPS was a mammalian (or perhaps yeast) PPI database? Is there another MIPS? Obviously E. coli will not be in the one that I'm thinking of.

Answer 1

[Fred Fleche]

http://www.kegg.jp/dbget-bin/www_bget?ath:AT1G15970

So you should have a look at the download section of Kegg if such information is:

1. Available in raw data file
2. Available for your species

[Sirus]

Oh, thank you, but only I couldn't find the download section could you please send me the link .

[Sirus]

I am looking for E.Coli protein list mapping

[Fred Fleche]

Here is the link : ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/eco/

[Sirus]

Thank you very much :).

[Sirus]

I have tried the link there is not MIPS entries I guess

[Sirus]

In other words I my proteins in this form PXXXX and I want it in the form Yxxxx and I think the MIPS IDs are in this written in this form

Answer 2

[Neilfws]

I've searched the web for MIPS and I cannot find anything that is relevant to E. coli. The only MIPS of which I'm aware is part of IBIS and I don't see anything there that relates to E. coli protein sequences.

Unless you can point to a MIPS entry on the web and /or explain why you think that Yxxxx is a MIPS identifier, I think it may be that MIPS is nothing to do with that organism.

[Sirus]

Well, me my self I am not that sure that they are MIPS ids, but I had searched from some annotations that are this form and found that they look like MIPS ones, but me too I am confused, because as you said the only available MIPS entries are for mamalian

[Sirus]

For example here it is a Yeast complex

[Sirus]

Well, actually, those Yxxxx are Ensemble Gene IDs, it took time to figure it out,