Question: Fasta Sequence For Each Hla Alleles
1
gravatar for J.F.Jiang
5.9 years ago by
J.F.Jiang800
China
J.F.Jiang800 wrote:

Hi all,

Since it is a new question for HLA typing, I post this question as new.

After trying several public tools, such as HLAminer and ATHLATES for HLA typing, it seems that the two tools are developed for whole-exome seq for the HLA genes. If we only seq some specific exons, it will not worked.

For example, we use Miseq to ONLY sequence the exon 2 and 3 for HLA-A gene, till now, my idea is to directly match the reads to the exon reference, because our reads length is 300bp while the exon length is ~270bp, in other words, one reads stand for a round of exon.

However, I am confused about the HLA database, for example, for HLA-A gene, it provides 2579 alleles. I can get the whole fasta file for each allele, but can not directly get the exon fasta data for each alleles.

The only similar file is the alignment file, A_nuc.txt, but I did not find any comments for this file. The HLA-A gene supposed to have 8 exons, does the file seperate these exons by "|"?If there is anyone know how to get the exon fasta data for alleles, plz let me know. HLA Class I Gene A B C E F G
Alleles 2,579 3,285 2,133 15 22 50 Proteins 1,833 2,459 1,507 6 4 16 Nulls 121 109 63 0 0 2

Thanks

fasta miseq • 3.6k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 5.9 years ago by J.F.Jiang800

You can try looking at the EMBL format IMGT/HLA data file which include the exon data (see ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat).

For more information about the data provided by IPD (including IMGT/HLA) I suggest you contact the IPD folks via their contact forms:

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Hamish3.1k

Thanks, I actually build a script to extract all the exon seq from the alignment file in IMGT

ADD REPLYlink written 5.9 years ago by J.F.Jiang800

Hi jing, which tool did you use finally for the data analysis ?

ADD REPLYlink written 5.8 years ago by geek_y10k

This is useful !!! others who wana extract HLA exomes information , I suggest you can use hla.dat to build your database.

ADD REPLYlink written 9 months ago by demolidd7740
1
gravatar for zam.iqbal.genome
5.9 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

I think the resource you want does not exist yet. IMGT contains information on the HLA classical genes restricted to 2 exons for class I, and 1 for class II (I think - don't quote me on class II). The _nuc files are from CDS (so with introns spliced out) and the _gen files are from genomic sequence (so have the introns). But I don't think there is available full sequence of the entire gene (all exons).

You might be interested in this paper:

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing Vinzenz Lange1†, Irina Böhme1*†, Jan Hofmann2, Kathrin Lang1, Jürgen Sauter2, Bianca Schöne1, Patrick Paul1, Viviane Albrecht1, Johanna M Andreas1, Daniel M Baier2, Jochen Nething3, Ulf Ehninger2,3, Carmen Schwarzelt1, Julia Pingel2, Gerhard Ehninger4 and Alexander H Schmidt1,2

in BMC Genomics, this year.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by zam.iqbal.genome1.7k

Thanks, I actually build a script to extract all the exon seq from the alignment file in IMGT

ADD REPLYlink written 5.9 years ago by J.F.Jiang800

Hi Jiang, which tool you are using for the data generated for only exon 2 and exon 3 ?

ADD REPLYlink written 5.8 years ago by geek_y10k

HI,geek_y, You can write a script to deal with hla.dat ,just to extract any HLA allele exons that you need .

ADD REPLYlink written 9 months ago by demolidd7740
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