Search Results for "patterns"

UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.

Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations.

...Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites requires the integration of various large-scale biological data in order to filter out false positives. PARSEC represents an intuitive, modular (easily extensible) and all-in-one solution for the efficient integration of lots of diverse genomic information in order to perform nonlinear localization and characterization of biological sites in a user-friendly environment. ...

The SPELL gene expression explorer searches multiple datasets for related gene expression patterns. Hibbs MA, et al. Exploring the functional landscape of gene expression: Directed search of large microarray compendia. Bioinformatics, 2007.

Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.