Getting Start


You need Mysql server running (local or distant) see: http://www.mysql.com/.
First, install (if not already installed) the "MySQL Server" (http://dev.mysql.com/downloads/).

A) First run blastall
:

Run blast with blastall application using the -m 18 (with Alignement) or -m 19 (without Alignement) output format option.
Example: blastall -i queries.fas -d subjects.fas -p blastn -m 18 -o queries_VS_subjects.bls
It produces 2 files one with the results: queries_VS_subjects.bls and one queries_VS_subjects.bls.par with blast parameters and some blast database descriptions.
ps: You can use the samples blast output results in the "samples_blast_results" folder.

B) Start jamblast


1) Setup the MySQL connection

Menu 'Config' -> 'Mysql'
This is done one time.
See: MySQL configurationfor more details.

1) Import the blast result in a database

Menu 'File' -> 'Open' Select the BLast results file.
You can use the demo file: queries_VS_subjects.bls located in the samples_blast_results folder.
Select it in the list (blast results set list) and click 'open Selected db'. You can optionally import query fasta file
ps: You can use the samples blast output results in the "samples_blast_results" folder.

See: Open/import helpfor more details.

2) Filter

Menu 'Filter & ort' -> 'Main Filter'
Set the filters criteria as you need
click 'Filter Evaluation' to validate your filter
and click 'Return to main' when you have finish.

See: Filter Help for more details.

3) Sorting

- You can sort unique Column by clicking the column header
- For multi columns sorting:
Menu 'Filter & Sort' -> 'Sort'
Add/remove column(s) in the list and select the sorting mode for each one (ascending or Descending)
Click 'Sort' to do the Sorting
and click 'Return to main' when you have finish.

See: Filter Help for more details.


4) Exporting hits in csv format

- To export filtered and sorted hits in csv format:
Menu 'File' -> 'Export'

See: Export Help for more details.

5) Exporting alignments hits in fasta format

To export alignments of selected hits in fasta format: select 1 or more hits and
Menu 'File' -> 'Export selected alignment'

See: Export Help for more details.

6) Save specific Queries sequences

- First you need to import in JAMBLAST the queries fasta file
Menu 'File' -> 'Import Queries fasta file'
and select the queries fasta file
- in the "Filtered Blast results" select 1 or more queries and right clik. A popup menu will appear. Select the "Save Queries Sequences" menu and enter a file name

See: Save queries sequences Help for more details.


General tips
- To see the tooltips move the mouse over fields.
- To display the popup menu right click in the grid.
- The columns can be reordered by clicking and dragging the column headers.
- The columns can be individually sorted by clicking the headers.
- The columns can be individually resized by clicking and dragging the column header's right border.
- The rows can be globally resized by clicking and dragging the top row header down border.
- You can copy the selected rows (multiple selections allowed) by holdind the "shift" or "ctrl" key with or without column headers and paste them directly in a spreadsheet.
- 'Ctrl+a': select all rows.
- 'Ctrl+c' copy the selected rows.