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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 Highlights

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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BLASTing local databases

SACS has a web interface to allow a user to BLAST a sequence aganist locally available blastable databases.

Available BLAST programs are blastp, blastn, blastx, tblastx and tblastn. This web interface is restricted to SACS subscribers. The user pastes in the desired fasta formatted sequence, selects the desired program and database from pull down menus, picks any desired options and then clicks the Submit button.

This BLAST interface uses software from NCBI's BLAST c++ toolkit and local SACS databases that are update weekly in most cases (swissprot and trembl are on a monthly basis).

Available databases are:
Protein databases Nucleotide databases
NCBI's nr NCBI's nt
UNIPROT's Trembl est_human, est_mouse, est_others
UNIPROT's SwissProt htgs, gss
refpro - RefSeq
(human, mouse, rat, zebra fish)
refnuc - RefSeq
(human, mouse, rat, zebra fish)
env_nr env_nt
pdbaa pdbnt
pataa patnt
month.aa month.nt

Gapped and ungapped output can be generated where the selected program permits.

Running BLAST searches locally will be slower than at NCBI as the local process is not threaded, the NCBI software appears to have problems dealing with large data files, and the SACS server does more than just run BLAST searches. The first time a selected databases is used in a web session the load time is much longer than subsequent uses. Be patient when doing a search. The interface has been written to keep the process alive until the BLAST search is finished.

[If you attempt a run and get a blank white screen, report this SACS along with the details about what you were trying to do so that the problem can resolved.]

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Tree Drawing

PHYLIP's Drawgram and Drawtree programs are available for use through a SACS web interface.

The general public can generate a basic tree image from a denogram data file, while SACS subscribers have more control over the process: selecting fonts and various orientation parameters.

The image on the left is from a Drawgram run presenting the denogram data as a swoopogram.

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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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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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