Table 1 Features of Genome2D*
From: Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data
Menu | Description |
|---|---|
File | Various input files (for example, FastA, GenBank, Glimmer, Paradox) can be loaded into Genome2D; contains commands to handle the program |
Blast | Window to perform blast searches on a local system or at NCBI and handle blast results (data extraction) |
Search | Algorithms to make a weight matrix (consensus sequence/motif); use weight matrix or input motif to screen loaded genome (see Example analysis: CcpA regulon in L. lactis) |
Drawing | Drawing of whole genome on linear map including additional information (promoter sites, terminators, regulator binding sites). Individual genes can be colored (manual selection). Changes in gene expression (multiple datasets in animation) are indicated by variation in color or number (see Application example: ComK regulon in B. subtilis) |
Tools | Algorithms for analysis of genomic DNA, randomization (statistical analysis) and extraction of coding or noncoding regions |
Boxes | Algorithms to analyze operons, upstream regions, box sequences and promoters. Custom adaptation of these algorithms is easily implemented (see example of K-box analyses [24]) |
Reformatting | Algorithms to convert files to another format |
Proteomics | Trypsin digestion on a database of proteins |