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August 30, 2016

Due to a change in the way NCBI names the download files on their server, the refseq and trembl databases are 2 weeks out of date. We are working on fixing this and will have new scripts in place by the end of September.

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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

Transmembrane Segments Prediction

SACS has three TMD predictions program (HMMTOP, Memsat and TMHMM) available for use through a SACS web interfaces.

These programs are open to the general public. The user supplies a fasta file for their protein of interest and the selected program makes a TMD prediction which is then displayed by TOPO2.

The TOPO2 can be used to generate a more sophisticated image of the predication by entering the generated prediction into its web interface by hand and then selecting from it numerous options to highlight residues of interest.

The image on the left is from a basic TOPO2 image of a TMHMM prediction for MXR (ABCG2).

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