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News

September 28, 2016

There has been some interest in having SACS host local copies of The Cancer Genome Atlas studies. If you would like to see us add this data to our databases, please contact scooter@cgl.ucsf.edu and let us know.

September 27, 2016

All BLAST databases have been updated to the latest releases from NCBI and the weekly scripts are now working with the new NCBI format.

September 25, 2016

BLAST updated to BLAST 2.4.0+. You should now use blastp and blastn rather than blastall.

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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


Gene Environment Resources

SACS has three web interfaces that allow a user to explore a gene's local genomic environment.

These programs are open to the general public. The user supplies a HGNC symbol for their gene of interest and the selected program then generates graphic output of the results.

Genes uses the HGNC symbol to locate the gene on a simple chromosome map of the species of interest (either human or mouse). A graphic show the location of the gene, it orientation (blue for a forward read and red a reverse read). Start and stop locations are given a table below the image. Gene families can be used in this program by entering in the beginning conserved portion of the family name (ie. use abc to find the locations of the ABC genes).

The gene envirnoments across 6 different species can be explored by using envs. In this case the graphic produced displays the location of the gene in human, rhesus monkey, mouse, rat, cow and dog. Ten genes either side of the desired one are displayed with their names and orientation given. A light gray band connects the highlighted gene accross the image. This way it can be easily check to see if the possible model species has the desired gene in the same orientation as the human, if there are naming differences between species or perhaps suggest another gene name to use in a search if the desired one is not found in a particular species. A table is given below the image showing gene names, and their start and stop points. A white band highlights the gene of interest in the table.

envs2 allows the selection of five animal model species in addition to human to explore genomic environments. The results are presented in the same manner as with the envs program.

The image at the left is from a envs run using the term abcb7. A gene with that name is not known in the dog and that area appears to be in the reverse orientation in the cow.

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