Hi,
I'm looking for a Macaca Mulatta KIR database. The data should be in the IPD database (http://www.ebi.ac.uk/ipd/index.html) according to paper the following paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808958/
Unfortunatelly, I can't see them there. Only Macaca mulatta MHC are there. Any suggestions where the data could be?
Please don't advise me to use GenBank instead. I really need reference sequences named according to official nomenclature. There are plenty of Macaca KIR sequences in GenBank, but their names are quite random :-(
Thanks,
Karel
Well, if you have not already, this could be a start. http://www.ebi.ac.uk/ipd/kir/
There are a list of KIRs in Allelelist.240.txt and Allelelist.250.txt which I believe corresponds with Macaca Mulatta, i.e. Mamu-KIR1D*002
Not as much a ready-to-use database, but, a quick grep yielded following list, hope this helps. It should be possible to collate these ids with other information withing the directory.
KIR00353 Mamu-KIR3DL1*013
KIR00354 Mamu-KIR3DL1*014
KIR00355 Mamu-KIR3DL1*015
KIR00356 Mamu-KIR3DL1*016
KIR00357 Mamu-KIR3DL10*003
KIR00358 Mamu-KIR3DL10*004
KIR00359 Mamu-KIR3DL1*017
KIR00360 Mamu-KIR3DL1*018
KIR00361 Mamu-KIR3DL20*001
KIR00362 Mamu-KIR3DL20*004
KIR00363 Mamu-KIR3DL20*005
KIR00364 Mamu-KIR3DL2*003
KIR00365 Mamu-KIR3DL2*00401
KIR00366 Mamu-KIR3DL2*00402
KIR00367 Mamu-KIR3DL2*005
KIR00368 Mamu-KIR3DL7*003
KIR00369 Mamu-KIR3DL7*004
KIR00370 Mamu-KIR3DL7*005
KIR00371 Mamu-KIR3DL7*006
KIR00372 Mamu-KIR3DL7*007
KIR00373 Mamu-KIR3DL7*008
KIR00375 Mamu-KIR3DL8*00102
KIR00376 Mamu-KIR1D*002
KIR00377 Mamu-KIR3DH2*00501
This is another clue that Macaca sequences should be there. But they are not. Mamu stands for Macaca with no doubt.
Unfortunately, for Allelelist.250.txt file there is no corresponding fasta file with sequences. For Allelelist.240.txt there is corresponding fasta file with all sequences except for Mamu ones.
That's sad :-(
Well, KIR Macaca sequences aren't right in IPD database (http://www.ebi.ac.uk/ipd/index.html), but can be found there by its search tool. The tool found 180 nucleotides sequences in ENA database, or 78 protein sequences in UniParc database. Unfortunatelly, it seems the sequences can be only downloaded one by one. Still better than nothing.
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