Tuneup Alignment Submission Form

Create or Tune Up a Multiple Alignment
This form will let you create or improve a multiple sequence alignment using hidden Markov models and the SAM system. Depending on the size of your query, processing can take seconds to hours, so you will receive the improved multiple sequence alignment via email.

Note: this page is quickly becoming obsolete, having been superseded by the more accurate and more featureful SAM-T99 tuneup web page.

E-mail Address (Required) for results:


Sequence type: nucleotide or protein

Place your multiple alignment or sequences in the box. Use the scroll bar on the right to make more room.



Return alignment in a pretty format , fasta format , or both fasta and pretty.

Sequence format is important. SAM uses D.G. Gilbert's ReadSeq package.
Be sure sequences are separated appropriately and that there is a newline at the end of your paste.

For example:
>Seq1
VTISCTGSSSNIGAG-NHVKWYQQLPG
>Seq2
VTISCTGTSSNIGS--ITVNWYQQLPG
>Seq3
LRLSCSSSGFIFSS--YAMYWVRQAPG

You may want to consult the online documentation or (view) download a postscript copy. The quick overview is particularly helpful.

Email sam-info@cse.ucsc.edu with problems and questions.
UCSC Computational Biology Group

SAM Home Page

sam-info@cse.ucsc.edu

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