1. What is SCOOTaR?

SCOOTaR (Sequence Comparison Output Organizing Tool and Repository) is an Open Source web-based tool for organizing and searching Sequence Comparison Outputs from programs such as BLAST, FASTA, and HMMER. It is useful for organizing search results when these results are large due to the number of sequences queried and/or the number of hits found. Hits may be organized into separate tables based on e-values, match lengths, or percent identity scores. Hit descriptions can be filtered and included or excluded from the result display. The number of 'best hits' displayed can be specified.

The search results are deposited into a MySQL database for querying. Graphical or textual alignment views are provided, as are links to external databases containing the matching sequences. SCOOTaR allows users to assign a rank and an annotation to each individual result, and output subsets of results to tab-delimited text files suitable for opening in Excel or OpenOffice.

2. What are the requirements for using SCOOTaR?

Users must have a mySQL login on the BCF amadeus server.  The mySQL login can be requested on the BCF Account RequestForm: http://bcf.arl.arizona.edu/online-tools/new-account-form.html or by sending email to This e-mail address is being protected from spam bots, you need JavaScript enabled to view it if you have an existing account.

3. How do I get started with SCOOTaR?

There are two possible ways to use SCOOTaR, depending on the size of the BLAST outputs you need to load. If you have a BLAST output that is smaller than 5Mb, BCF can simply create a mySQL login for you and you can load the BLAST report into SCOOT from your web browser (email This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ).

If you need to load larger BLAST output files, you will need a Biodesk account on our amadeus server. You can apply for this account here: http://bcf.arl.arizona.edu/online-tools/new-account-form.html.   Make a note that you would like to use SCOOTaR and when your account is created it will include the mysql login that SCOOTaR requires. If you need help learning some basic UNIX commands, see http://bcf.arl.arizona.edu/unix-tutorials

4. How do I load a BLAST/FASTA/HMMER output into SCOOTaR?

As indicated in the answer above, there are two methods. For an output smaller than 5Mb, simply go to http://scoot.biosci.arizona.edu and click the 'SCOOT' Tab and the 'Load Report' Tab. For larger files, login to amadeus and use the command 'loadscoot -v mysql_login /home/mydept/mylogin/myfile.bln myproject', where the italicized items are replaced with your mysql login, the full path to your comparison output file, and a SCOOTaR project name.

5. How do I run BLAST/FASTA/HMMER on a large number of sequences?

See http://bcf.arl.arizona.edu/high-throughput-computing/hpc-blast

6. How do I get more help with SCOOTaR?

First click the SCOOTaR 'User Manual' Tab and read the information there. To set up custom links in SCOOTaR or ask questions that are not answered here or in the manual, contact Susan Miller ( This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ).