Table 1 This table summarizes the inputs and outputs for InDeVal. It provides the names of the different InDeVal file types and displays, the number involved in analyzing a single portion of DNA, whether or not they are required for InDeVal function, their basic format, whether or not they are provided with the InDeVal package, when they are produced, and a brief description.
Input | Number | Required | Format | Provided | Description |
|---|---|---|---|---|---|
Conserved region file | One | Yes | InDeVal-specific | Yes | Representative sequence with variable regions replaced by variable region file names |
Variable region file | Multiple | No | InDeVal-specific | Yes (28) | List of sequences for which a variable region is to be searched and a message to be displayed for each |
DNA sequence file | One | Yes | FASTA | No | Set of sequences to be analyzed |
Output | Number | Produced | Format | Description | |
Sequence Analysis Window | One per analyzed sequence | Always | Display | Displays analyzed sequence broken into user-defined units and allows InDeVal/user interaction | |
Variable Region Analysis Window | One per variable region | Upon user-request | Display | Displays one variable region so that the sequence found in the analyzed sequence can be contrasted with those found in all other studied sequences | |
Output file | One per analyzed sequence | Upon user-request | Similar to NCBI default display | Text file of the analyzed sequence, annotated with conserved and variable region positions and variable region sequence-specific messages | |