How can I view SAM-T02 results in graphical format?
The only graphical results from SAM-T02 are the sequence logos, which are all in EPS (Encapsulated Postscript) format. There are many programs available for viewing EPS files—which one you chose is largely a question of what platform you run on. The most popular viewer for Unix machines is the free “ghostview” program (also available for MS-Windows and Macs) http://www.cs.wisc.edu/~ghost/gsview/index.htm If you wish to see a 3D model of the predicted protein, you have to convert the alignment to a 3D structure. Although we are working on tools to do this, they are not yet ready for release. In the meantime, your best bet is to take the .al files and submit them to the AL2TS server: http://predictioncenter.org/local/al2ts/al2ts.html That server only accepts their own “.al” format, which we provide for just the alignments based on the 2-track-protein-STR hidden Markov models (these are usually the best alignments). • What do the sequence IDs in a SAM-T02 a2m file mean? Most of the sequ
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