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Help Home > Alignment Search > Running Alignment Search

Running Alignment Search

The default Alignment Search page is a basic form for submitting alignment queries. To modify the default search parameters, click the advanced settings link to the right of the Alignment Program menu. The page will reload to display the advanced program settings page.

The default (basic) Alignment Search page provides a selection of alignment programs and databases to choose from the pull-down menus. To run your alignment search, you will need to select the appropriate alignment program and database, and the sequence or sequences you would like to align.

To search for alignments using the default parameters' page:

  1. Select the alignment program you want to use (e.g., tblastn or blatn) from the Alignment Program menu.
  2. Select a database from the Database menu (only those compatible with your alignment program selection are shown.)
  3. Paste your sequence or multiple sequences, in FASTA format, in the Query Sequence box, and/or use the Browse button to select a sequence file from your computer.
  4. You can also choose to enter your email address in the Email Address (optional) box, and our system will notify you by email once your results are ready for viewing. NOTE: You do not need to supply an email address to conduct an alignment search.
  5. Click the Submit Job button to run your alignment search.

Waiting for Results

The current "average execution time" for the last 1,000 jobs is printed beneath the Submit Job button. This text will give you a rough estimate of the amount of time currently required to process an average alignment search. However, depending on the size of your query sequence(s) and target database size, it could take anywhere from 30 seconds to 5 - 10 minutes to complete your job.

Once you have submitted an alignment search request to our job queuing system, your request will be assigned a unique numerical job identification number (Job ID) and you will be automatically redirected to the job status page. If you also supplied an email address, our system will notify you by email once your job results are ready.

The Job Status page will automatically update every 10 seconds until your job has completed or failed. On failure, an error message will be produced and you are urged to contact us for assistance. Upon completion, you will be redirected to your results which will either be displayed graphically or as raw output depending on the target database type. You can bookmark the resulting URL for reference, however, your results will be available for up to two weeks.

Advanced Settings

Advanced alignment queries allow you to fine tune alignment program-specific parameters. These parameters vary for each alignment program. To switch from basic to advanced mode, click the advanced settings link. The alignment search system will automatically update to display the advanced settings for the tool you selected and allow you to update parameters such as the Expect value and word size for BLAST or the tile size for BLAT. For more information about how to set the parameters for each, see the home pages for relevant alignment program (NCBI's BLAST, and Jim Kent's BLAT).