STRETCHER (a part of EMBOSS package) calculates a global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space. A global pairwise alignment is one where it is assumed that the two sequences have diverged from a common ancestor and that the program should try to stretch the two sequences, introducing gaps where necessary, in order to show the alignment over the whole length of the two sequences that best illustrates their similarities. For more information about STRETCHER visit this page or the EMBOSS site.

Our installation of STRETCHER allows for "massive" pairwise alignments of each sequence from one set (the query) to each sequence from the second set (the reference). You will need to upload the query and the reference sets in fasta format. You can also specify additional program options.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

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E-mail:  (only guests need to use this field, registered users should log in)

Job name:   (please, no spaces, special characters etc., uderscore is OK)

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Query fasta file:
  
Reference fasta file:



Program options: all standard options related to input and output file names will be supplied automatically. Below you may specify additional STRETCHER options controling the alignment, such as -datafile, -gaplength, -gappenalty, or    -aformat3.

Additional STRETCHER options (if left blank, defaults will be used):
NOTE: correctness of your options line will NOT be verified before job submission!

I am a TAIR member
(if this box is checked, output files will have to be retrieved from a special FTP account instead of links in notification e-mails)

Number of processors to use 
(with small number of processors the job may start sooner, but it may take more time to complete)

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Cluster: This application can't run at this time - no suitable clusters
or you are not authorized to use the service.
The service is available only to Cornell students, faculty, and staff.   ( Show timeout info )

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