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July 9, 2011

Release 184 for both GenBank and GenPept is now available in sequence format.

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The mission of the Sequence Analysis & Consulting Service (SACS) is to bring visualization, networking, computional and bioinformatic tools to the UCSF research community. These tools provide methods for characterization and interpretion of genomic data, including nucleic acid and protein sequence analysis, pharmacogenomics and data mining. As part of the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI), SACS provides its services primarily on a recharge basis to UCSF researchers. Collaborations may also be possible.

Resource Highlight

Alignment Resources

There are a number of alignment programs available for use through SACS web interfaces.

These programs are open to the general public. The user supplies a fasta file for their sequences of interest and the selected program then generates an alignment.

There are four pairwise alignment programs: needle and stretcher which preform global alignments plus matcher and water which preform local alignments.

Multiple alignments are handled by clustalw, multalin, muscle and t_coffee. The multalin and t_coffee programs produces colored images of their alignments. Clustalw, multalin and t_coffee produce files that can be used in the drawgram or drawtree interfaces.

The image at the left is from a t_coffee run.

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