What is the diff between kir3ds1_gen kir3ds1_nuc

arkilis · 01-11-2015, 10:49 PM

I am currently doing the kir alignment, but found there are two nucleotide sequence files on ftp://ftp.ebi.ac.uk/pub/databases/ipd/kir/ for a specific a locus:

i.e. kir3ds1_gen and kir3ds1_nuc. which one should I use? can not find related explanation in the readme file.

Also there is a overall file named KIR_nuc.fasta. but which seems not a sum up file joined by all locus?

Any tips? Thanks!

GenoMax · 01-12-2015, 05:18 AM

It appears that

*_gen = genomic sequence
*_nuc = exons/CDS

Depending experiment your reads were derived from/questions you want to ask choose accordingly.

arkilis · 01-12-2015, 03:13 PM

Thanks GenoMax again. You helped me on the other question. I might want to find out the all kir genes in a batch of sequence data.

When I go the the ftp site, I found kir_nuc.fasta and many other individual locus sequences (i.e. kir3ds1_nuc.fasta), the kir_nuc.fasta name seems to be an all-in-one sequence file. But when I concatenate all the other locus sequence, which the sequence content is different from kir_nuc.fasta. So if I want to find all kir genes, should I use the kir_nuc.fasta or create a new one which concatenate all single locus sequence together?

Many thanks!

GenoMax · 01-12-2015, 04:11 PM

I am going to suggest that you contact IPD support to see if you can get an authoritative answer: http://www.ebi.ac.uk/support/ipd.php

You could blast the kir_nuc.fasta against the concatenated file to see if everything is represented in the large single file. My hunch is that it is likely true.

arkilis · 01-12-2015, 04:20 PM

Quote:

Originally Posted by GenoMax

I am going to suggest that you contact IPD support to see if you can get an authoritative answer: http://www.ebi.ac.uk/support/ipd.php

You could blast the kir_nuc.fasta against the concatenated file to see if everything is represented in the large single file. My hunch is that it is likely true.

Thanks mate!

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01-11-2015, 10:49 PM	#1
arkilis Senior Member Location: Australia Join Date: Jul 2013 Posts: 119	What is the diff between kir3ds1_gen kir3ds1_nuc I am currently doing the kir alignment, but found there are two nucleotide sequence files on ftp://ftp.ebi.ac.uk/pub/databases/ipd/kir/ for a specific a locus: i.e. kir3ds1_gen and kir3ds1_nuc. which one should I use? can not find related explanation in the readme file. Also there is a overall file named KIR_nuc.fasta. but which seems not a sum up file joined by all locus? Any tips? Thanks!

01-12-2015, 05:18 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	It appears that _gen = genomic sequence _nuc = exons/CDS Depending experiment your reads were derived from/questions you want to ask choose accordingly.

01-12-2015, 03:13 PM	#3
arkilis Senior Member Location: Australia Join Date: Jul 2013 Posts: 119	Thanks GenoMax again. You helped me on the other question. I might want to find out the all kir genes in a batch of sequence data. When I go the the ftp site, I found kir_nuc.fasta and many other individual locus sequences (i.e. kir3ds1_nuc.fasta), the kir_nuc.fasta name seems to be an all-in-one sequence file. But when I concatenate all the other locus sequence, which the sequence content is different from kir_nuc.fasta. So if I want to find all kir genes, should I use the kir_nuc.fasta or create a new one which concatenate all single locus sequence together? Many thanks!

01-12-2015, 04:11 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	I am going to suggest that you contact IPD support to see if you can get an authoritative answer: http://www.ebi.ac.uk/support/ipd.php You could blast the kir_nuc.fasta against the concatenated file to see if everything is represented in the large single file. My hunch is that it is likely true.