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Other ParametersRangeRange is designed to be specified when dealing with a large number of input sequences. If a file contains many sequences, you can acheive alignment for all of them by running iHMMune-align several times and providing a range of sequences for which results should be returned. For example, if an input file contained 200 sequences. The first 'run' of iHMMune-align could be called for a range of 1 to 50, then subsequent runs for 51 - 100, 101 - 150 and finally 151 - 200. It is advised that no more than 100 sequence be attempted in a single request to iHMMune-align to prevent over burdening the server. Processing of large sets of sequences is best suited to a local execution of iHMMune-align.IGHD Minimum LengthThe identification of IGHD genes is complicated by their short length, the presence of mutations, nucleotide loss from both ends and the presence of the N-additions both upstream and downstream. Minimum criteria can be set for the identification of the D-REGION. Currently, the options are based on a minimum IGHD length without any mismatches. This can be set to a minimum length of 5 or 8 nucleotides. Please see (1) and (2) for discussion of the confident identification of the D-REGION.The option also exists for the dynamic determination of IGHD identification. This is based on the results of studies outline in 1. Briefly, the frequency at which sequences that mimicked mutated D-REGIONs occurred within N-REGIONs were calculated. This was possible through characterisation of the N-additions and modelling of the additions to create large simulated datasets. Frequencies were then derived using the large simulated sets. The probabilities are dependent on the length and mutations within the D-REGION and then length of the region between the IGHV end and the start of the IGHJ. For this reason this approach is referred to as dynamic as it depends on the context of the partitioning. A threshold of 0.001 is used to determine confidence of D-REIGON partitioning. References
1. K. J. L. Jackson, Gaeta, B. A. and Collins, A. M., 2007,
Identifying highly mutated IGHD genes in the junctions of rearranged human immunoglobulin heavy chains , Journal of Immunological Methods,
doi:10.1016/j.jim.2007.04.011
2. A. M. Collins, Ikutani, M., Puiu, D., Buck, G. A., Nadkarni, A. and Gaeta, B., 2004, Partitioning of Rearranged Ig Genes by Mutation Analysis Demonstrates D-D Fusion and V Gene Replacement in the Expressed Human Repertoire , Journal of Immunology, 172:340-348 |
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