SEWAL
|
Application data |
|
| Biological application domain(s) | in vitro selection |
|---|---|
| Technology | Illumina |
| Maintained? | Maybe |
Summary: Processing of deep sequencing data from in vitro selection experiments
"Error: no local variable "counter" was set." is not a number.
Description
Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (108 sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (107 sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets.
Links
References
To add a reference for SEWAL, enter the PubMed ID in the field below and click 'Add'.
Search for "SEWAL" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
