• Sbg
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Graphical Version
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Command Line Version
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Usage

After downloading the application and start with

java -jar /path/to/sbg.jar

in a terminal.

Input

This application takes a set of blast output of the following format

Column	Name
0	query name
1	subject name
2	percent identities
3	aligned length
4	number of mismatched positions
5	number of gap positions
6	query sequence start
7	query sequence end
8	subject sequence start
9	subject sequence end
10	e-value
11	bit score

The bold columns are neccessary for the program to work. This format is "blast -m8", see here and search for "Blast -m8 fields".

Example

SAM50_AMEBA     SAM50_AMEBA     100.00  118     0       0       1       118     1       118     9e-67    243
SAM50_AMEBA     gi|126338997|ref|XP_001362470.1|        29.66   118     70      4       3       115     151     260     4e-09   52.4
SAM50_AMEBA     gi|114686851|ref|XP_001172164.1|        28.81   118     71      4       3       115     72      181     1e-08   50.8

Generated Graphs

The generated lines are ordered in 3 different ways. The lines have the information about the sequence, the start and end positions where the fragment was found.