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. 2004 Jul 1;32(Web Server issue):W173-5.
doi: 10.1093/nar/gkh424.

The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences

Wolfgang Helmberg  1 , Raymond Dunivin, Michael Feolo
Affiliations

The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences

Wolfgang Helmberg et al. Nucleic Acids Res. .

Abstract

The dbMHC resource (http://www.ncbi.nlm.nih.gov/mhc/sbt.cgi?cmd=main) at the National Center for Biotechnology Information (NCBI) has developed an online tool for evaluating the allelic composition of sequencing-based typing (SBT) results of cDNA or genomic sequences. Whether the samples are heterozygous, haploid or a combination of the two, they can be compared with two up-to-date databases of all known alleles of several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) loci. The results of the submission are returned as a table of potential allele hits, along with the respective base changes and an interactive sequence viewer for close examination of the alignment.

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Figures

Figure 1
Figure 1
The interface of the SBT resource. The page is divided into two frames. The top frame contains the submission form and displays the interpretation results; the bottom frame contains the interactive alignment viewer. In this example are three query sequences (Query 1–3), all testing the HLA-A locus from one sample. ‘Query 1’ and ‘Query 2’ are haploid, whereas ‘Query 3’ is heterozygous. One nucleotide mismatch is allowed between the query and matched sequences. Two allele combinations match perfectly; four allele combinations show one mismatch each. The blockwise display of the query sequences starts with ‘Query 1’. Nucleotides 1–270 of ‘Query 1’ are part of exon 2. The bottom frame shows the three query sequences aligned to the reference sequence A*010101. The mismatch for the allele combination A*0102–A0103 at position 363 (A<>A,G) is highlighted. The nucleotide ‘A’ in the heterozygous ‘Query 3’ does not match with the combination A,G of A*0102–A0103.
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