Evaluation of IGH partitioning tools

Application of inferred genotypes to the evaluation of IGH partitioning tools


IGH partitioning evaluation tool:

Evaluations are performed against individual genotypes inferred from high throughput sequencing (as described in Boyd, 2010). To use the evaluation tool, obtain the Stanford_S22 dataset and perform IGH partitioning using the utility of your choice. Sets of results for the Stanford_S22 dataset, generated using a number of IGH utilities, are available on the datasets page, along with links to access the various utilities. The partitioning results produced by a utility can then be compared to an inferred genotype by either pasting results into the text box below, or indicating a file for upload. The formatting requirements for input files a file are described here.

The evaluation tool will provide details of the allocation of genes and allelic variants absent from the inferred genotype for the IGHV, IGHD and IGHJ.

References:

For information regarding inference of genotypes from high throughput sequencing:
Boyd, S.D., et. al., 2010, Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements,184, 6986 -6992
For information regarding the use of the Stanford_S22 dataset and its associated genotype as a tool for IGH partitioning utility evaluation:
Jackson, K.J., et. al., 2010, A gold standard for the evaluation of human immunoglobulin gene alignment utilities, Submitted

IGH utility evaluation
Contact

For queries:
Andrew Collins
Katherine Jackson



    

Enter utility partition results or select an input file:

 Paste results into the box below:


 Use the 'Browse...' button to locate a results file:

Genotype:



genotype to be used for evaluation.

If custom genotype requested, please specify file containing the genotype: 

Additional options:



Consider all equal scoring genes:  Yes
 No
Provide details of incorrect assignment of genes:  Yes
 No