ABSTRACT
Abstract ................................................................................................. 224 9.1 Introduction .................................................................................. 224 9.2 High-Throughput Sequencing Data Cleaning Tools .................... 225 9.3 GL Segment Identification Tools and Junction Analysis ............. 227 9.4 Finding Clones ............................................................................. 228 9.5 Alignment .................................................................................... 229 9.6 Repertoire Presentation ................................................................ 229 9.7 Lineage Trees ............................................................................... 232 9.8 Motif Analysis .............................................................................. 232 9.9 Mutation Statistics ....................................................................... 233 9.10 Testing For Selection ................................................................... 234 9.11 Automation .................................................................................. 235 9.12 Concluding Remarks .................................................................... 236 Keywords .............................................................................................. 236 References ............................................................................................. 236
ABSTRACT
Analyzing immunoglobulin gene sequences, especially in the high throughput sequencing age, raises many challenges. The diverse repertoire and somatic hypermutation they undergo differ the immunoglobulin sequences from other genes, making the commonly used tools unfit for their analysis. Unlike the other genes, immunoglobulins lack a reference gene, raising problems in cleaning the high throughput sequences and defining the germline sequence that will be used as such. Clustering into clones and repertoire representation are nonexistent issues when dealing with uniform genes, but are key analyzes while dealing with immunoglobulin’s. This chapter is a thorough review of the informatics tools that were designed to address the unique nature of the immunoglobulins.
