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:5) Exporting alignments hits in fasta format
To export alignments of selected hits in fasta format: select 1 or more hits and6) Save specific Queries sequences
- First you need to import in JAMBLAST the queries fasta file