Genomics and Next Generation Sequencing

Over the past few decades, genomics has become a key technology for deciphering life’s code and for engineering phenotypes.

As sequencing costs continue to drop and workflows become increasingly automated, researchers need to make sense of ever larger sets of data about individuals or groups of organisms. They need to decipher relationships between these sequences and their function in health and disease.

MATLAB^®provides a platform for researchers working withbiological sequencedata including common algorithms for autocorrelation, BLAST, Needleman-Wunsch, global sequence alignment, whole genome comparison, and read counting. Researchers can read data from multiplesequence databasessuch as KEGG and NCBI. MATLAB provides related capabilities includingstatisticsormachine learning,visualizing molecules, andGPU support. As a result, a global community of scientific researchers and bioinformatics professionals have developed and shared a broad range of open-source toolboxes written in MATLAB.

Community Apps and Toolboxes

• Bmix: Identification of RNA interaction sites of a protein
• BOBA FRET: Tethered single-molecule FRET data analysis
• DeAnnCNV: Number variations from whole-exome sequencing
• DeltaProt: Comparative genomics
• ESCAPE: Integration of high-content stem cell data
• FastMotif: Sequence motif discovery
• FUGA: Analysis of complex biological networks
• GeneNet Toolbox: Analysis of connectivity in gene networks
• GWAS-NR version 2.0: Identification of correlations of multiple genomic regions
• Magenta: Genetic associations in functionally related genes
• MATLABStarter: A series of startup functions for MATLAB to set up a multi-user environment
• MBEToolbox 2.0: DNA and protein sequence analysis
• MCaVoH: Cluster 16S rRNA sequence data
• MEIGO: Global optimization in systems biology
• MSKCC CGDS Cancer Genomics Toolbox: Cancer genomics server at MSK
• OncoSNP-SEQ: Identification of somatic copy number alterations in NGS data
• PGEToolbox: Population genetics and evolution
• PROPER:排名高的评价sifiers for data mining
• RVD:罕见的单核苷酸变异的检测
• SEK: Estimation of bacterial community composition
• spads 1.0: Population genetic variability
• WaveCNV: Identification of copy number alterations in tumors

User Stories

• Centers for Disease Control and Prevention Automates Poliovirus Sequencing and Tracking
• Massachusetts Institute of Technology Integrates Cancer Research in the Lab and Classroom

Technical Articles and Examples

• Analyzing Array-Based Comparative Genomic Hybridization Data
• Identifying Differentially Expressed Genes from RNA-Seq Data
• Working with Whole Genome Data
• Bioinformatics Toolbox Examples
• Cancer Detection Examples
• Batch Processing of Spectra Using Sequential and Parallel Computing