Install all AlignDB requirement software and dependent Perl modules. Read the README file in the AlignDB package root directory.
Install AlignDB itself. Follow the steps in doc/tutorial.pdf and use the example data in data/ directory coming with AlignDB for a trial run.
Prepare a set of input data in Blastz .axt file format. For example, you can download the completed genomic alignments from the UCSC Genome Bioinformatics Site.
- Starting the GUI shell. Enter the base directory where you installed AlignDB. Type the follow command:
The GUI interface shows in Fig.1. DO NOT close the command line window, AlignDB need it.
- Two-way comparison steps.
Step 1: test your server. Click on the “DB Server” notebook tab, and check MySQL server setting.
Step 2: initiate your database. Then click the “Init. alignDB” button, which will call init\init_alignDB.pl to build the skeleton of the database.
Step 3: generate two-way analysis database. Click the “Gene. alignDB” button which will call init\gene_alignDB.pl to analysis alignments and build the database.
Step 4: update features using Ensembl annotations. Click the “Feature” tab, change nothing and click the “Upd. feature” button, which will run init\update_feature.pl.
Step 5: update misc features. Click the “Misc” tab. Click “Upd. slippage” to run init\update_indel_slippage.pl and then click “Upd. isw” to run init\update_isw_indel_id.pl.
Step 6: do statistics and get results. Then click “Common stat” button. An Excel workbook with 25 worksheets will be generated.
Step 7: charting. If you run AlignDB on Windows, just like me, you could click the “Common chart” button, which will run stat\common_chart_factory.pl that call Excel to draw charts in .xls files by OLE. Fig.2 is an example workbook.
- Three-way comparison steps.
Three-way comparison needs three genome sequences to accomplish. So you should add a new genome sequence into the previous two-way comparison. This can be accomplished by joining two two-way comparisons, which share a common target sequence.
Step 1: build another two-way comparison. You can just do steps 1-3 and omit step 4-7 if you don’t need statistical analysis for the new two-way database.
Step 2: generate three-way analysis database. Load two completed databases into “first db” and “second db”. Generate “goal db” name with the default naming rule. Leave the “T/Q/R:” options unchanged, and click the “Ref outgroup” button. See Fig.3 for an example.
Step 3: update two-way features. Three-way comparison database is also a legal two-way database. Do step 4-5 of two-way comparison to update the new three-way database.
Step 4: update three-way features. Go to “Misc” tab in the “Three-way” pane and click the “Upd. CpG” button to run extra\update_snp_cpg.pl.
Step 5: do statistics and get results. Then click “Three stat” button which will run stat\three_stat_factory.pl. An Excel workbook with 11 worksheets will be generated.
Step 6: charting. This step is almost the same as step 7 in Two-way comparison. Just click the “Three chart” button, which will run stat\three_chart_factory.pl.